Geneious Prime Changelog

What's new in Geneious Prime 2024.0.5

Apr 16, 2024

Fixed long delays when trying to load contigs

New in Geneious Prime 2024.0.4 (Mar 27, 2024)

New in Geneious Prime 2024.0.3 (Mar 6, 2024)

New in Geneious Prime 2024.0.2 (Feb 15, 2024)

New in Geneious Prime 2024.0.1 (Feb 15, 2024)

New in Geneious Prime 2024.0 (Feb 15, 2024)

New in Geneious Prime 2024.0.1 Beta (Jan 31, 2024)

New in Geneious Prime 2024.0.0 Beta (Dec 6, 2023)

New in Geneious Prime 2023.2.1 (Jul 25, 2023)

New in Geneious Prime 2023.2.0 (Jul 25, 2023)

New in Geneious Prime 2023.1.2 (Apr 28, 2023)

New in Geneious Prime 2023.1.1 (Apr 7, 2023)

New in Geneious Prime 2023.1.0 (Apr 7, 2023)

New in Geneious Prime 2023.1.0 Beta (Feb 22, 2023)

New in Geneious Prime 2023.0.4 (Feb 21, 2023)

New in Geneious Prime 2023.0.3 (Feb 21, 2023)

New in Geneious Prime 2023.0.2 (Feb 21, 2023)

New in Geneious Prime 2023.0.1 (Feb 21, 2023)

New in Geneious Prime 2023.0.0 (Feb 21, 2023)

Features:
CRISPR: Added more PAMs to Find CRISPR Sites
Cloning Validation: Added a new tool for automating sequence alignment during batch plasmid validation
Primer Design: Added a new tool for primer specificity testing
STAR: Added STAR, a RNA-seq mapper that performs highly accurate spliced sequence alignment
Workflows: Added new workflow for batch exporting multiple sequences as individual images
Minor Features and Usability Improvements:
CRISPR: Enabled selection of individual off-target sequences
Command Line Interface: Now supports using database folders as inputs
Geneious Academy: Added a shortcut to the new Geneious Academy in the Help menu
General: Progress reporting for loading selected documents on network databases no longer blocks user activity
Preprocessing: BBDuk no longer requires a separate plugin to use
User Interface: Dropdowns now support filtering and more clearly show when it is possible to enter custom value
Fixes and Minor Changes:
Bowtie2: Updated to Bowtie2 2.4.5
CRISPR: Added a maximum gap size option to Analyzing CRISPR Editing Results
Command Line Interface: Fixed bug where documents in the local database could not be found
Dark Mode: Brightened the Sequence Viewer selected number color
De Novo Assembly: Fixed it sometimes producing results containing mismatches when the maximum mismatches settings was set to 0
De Novo Assembly and Map to Reference(s): Now fails promptly instead of sometimes continuing after running out of memory
Group Sequences: Fixed crash when grouping protein sequences together with paired nucleotide sequences
MAFFT: Updated MAFFT to version 7.490
MUSCLE: Updated MUSCLE algorithm to version 5.1
Memory: Reduced memory usage when dealing with some large data sets
SPAdes: Updated SPAdes to version 3.15.5
Sample Documents: Added the SARS-CoV-2 genome
Sequence View: Added option to turn off three letter amino acids when zoomed in on protein sequence views
Shared Database: Updated default mysql-connector to 8.0.28
Shared database: Fixed a bug where indexing of documents in shared databases would not proceed due to a corrupt document
Startup: Added a progress bar to show progress starting Geneious
Annotations:
Fixed a crash when exporting an annotation table with the "Paired Primer" column
Fixed pressing delete in the Annotations Table sometimes not deleting the selected annotation(s)
General:
Reformatted concatenated file names when spacers used
Creating or renaming a folder will ask for another name in the event the provided name was invalid
Added a Save as PDF... option to the File menu
Fixed crash when batch renaming very large sequence lists
Improved document save performance, especially on network databases
Fixed a rare crash when gathering system information during start-up
Other Notes:
16S Biodiversity: Removed the 16S Biodiversity tool
Plugin Development Kit: Fixed return behaviour for DocumentUtilities.getDocumentsByURN() not matching its javadoc
Public API: Added an API to add stamps to items in dropdowns
TopHat: Removed TopHat RNAseq mapper

New in Geneious Prime 2023.0.0 Beta (Nov 2, 2022)

Features:
CRISPR: Added more PAMs to Find CRISPR Sites
Cloning Validation: Added a new tool for automating sequence alignment during batch plasmid validation
Primer Design: Added a new tool for primer specificity testing
STAR: Added STAR, a RNA-seq mapper that performs highly accurate spliced sequence alignment
Workflows: Added new workflow for batch exporting multiple sequences as individual images
Minor Features and Usability Improvements:
CRISPR: Enabled selection of individual off-target sequences
Command Line Interface: Now supports using database folders as inputs
Geneious Academy: Added a shortcut to the new Geneious Academy in the Help menu
General: Progress reporting for loading selected documents on network databases no longer blocks user activity
Preprocessing: BBDuk no longer requires a separate plugin to use
User Interface: Dropdowns now support filtering and more clearly show when it is possible to enter custom value
Fixes and Minor Changes:
Annotations:
Fixed a crash when exporting an annotation table with the "Paired Primer" column
Fixed pressing delete in the Annotations Table sometimes not deleting the selected annotation(s)
Bowtie2: Updated to Bowtie2 2.4.5
CRISPR: Added a maximum gap size option to Analyzing CRISPR Editing Results
Command Line Interface: Fixed bug where documents in the local database could not be found
Dark Mode: Brightened the Sequence Viewer selected number color
De Novo Assembly: Fixed it sometimes producing results containing mismatches when the maximum mismatches settings was set to 0
De Novo Assembly and Map to Reference(s): Now fails promptly instead of sometimes continuing after running out of memory
General:
Reformatted concatenated file names when spacers used
Creating or renaming a folder will ask for another name in the event the provided name was invalid
Added a Save as PDF... option to the File menu
Fixed crash when batch renaming very large sequence lists
Improved document save performance, especially on network databases
Fixed a rare crash when gathering system information during start-up
Group Sequences: Fixed crash when grouping protein sequences together with paired nucleotide sequences
MAFFT: Updated MAFFT to version 7.490
MUSCLE: Updated MUSCLE algorithm to version 5.1
Memory: Reduced memory usage when dealing with some large data sets
SPAdes: Updated SPAdes to version 3.15.5
Sample Documents: Added the SARS-CoV-2 genome
Sequence View: Added option to turn off three letter amino acids when zoomed in on protein sequence views
Shared Database: Updated default mysql-connector to 8.0.28
Shared database: Fixed a bug where indexing of documents in shared databases would not proceed due to a corrupt document
Startup: Added a progress bar to show progress starting Geneious
Other Notes:
16S Biodiversity: Removed the 16S Biodiversity tool
Plugin Development Kit: Fixed return behaviour for DocumentUtilities.getDocumentsByURN() not matching its javadoc
Public API: Added an API to add stamps to items in dropdowns
TopHat: Removed TopHat RNAseq mapper

New in Geneious Prime 2022.2.2 (Nov 2, 2022)

New in Geneious Prime 2022.2.1 (Nov 2, 2022)

New in Geneious Prime 2022.2 (Nov 2, 2022)

Features:
CLI: Added support to import and export files from local databases
CLI: Added support to import and export files from shared databases
Cloning: Added In-Fusion cloning
Parts Cloning: Added support for protein documents
Primer Import: Added the ability to automatically annotate primer extensions on import if provided appropriately formatted sequences
Minor Features and Usability Improvements:
3D Protein viewer: Updated Jmol to version 6
Cloning:
Improved input validation for batch operations
Improved the cloning options dialog
Improved the naming scheme for sequence list results of cloning operations
Other various UI/UX improvements
User Interface:
Added filter functionality to combo box components with 10 or more values
Added floating name column to document and annotation tables
Fixes and Minor Changes:
Advanced Preferences: Fixed advanced preference table values not being reloaded after changes
Apply Variants to Reference Sequence: Added option to mask low coverage regions with N
BLAST:
Fixed bug where changing options in BLAST workflows for one blast type affected other blast type options
Chromatogram Viewer: Fixed a bug where some Color Schemes were showing incorrect line and text colors
Cloning:
Fixed a bug where cloning results had the wrong insert order in their names
Fixed canceling operations
Fixed rare crash where rearranging cloning inserts in restriction cloning
Operations should now perform significantly faster on large datasets
Sequence Lists are now reversed correctly in Golden Gate cloning
Sequence Lists produce correct lineage interval in Golden Gate cloning
Command Line Interface:
Added parameter --installationId to display installation id in command line
CRISPR:
Better detection of pre-installed python3
Fixed annotation colors not showing up sometimes when Find CRISPR Sites is run on sequence lists
Prevented attempts to install an incompatible version of python
Databases
Improve performance when copying multiple documents and folders in the local database
Geneious Server: Now ensures python3 is available for SPAdes
General:
Added a button to hide/show text on all password fields
Added ability for admins to disable arbitrary plugins
Fixed a bug where ctrl+drag (or alt+drag) documents into the same folder and choosing 'Replace' deletes these documents
Fixed occasionally being unable to uninstall Geneious
Fixed a rare crash when gathering crash information
High/Low Coverage Finder: Changed annotation type to be always "Coverage - Low" instead of sometimes "Coverage - Low" and sometimes "Low" and likewise for high coverage annotations
Import/Export:
Fixed a bug where document and folder chooser dialogs do not appear when Grammarly Desktop is installed or system screen zoom settings are enabled
Fixed rare crash when importing vcf files with malformed meta-info data
Geneious now sorts sequence annotations by sequence start index when exporting in GFF and BED file formats
Sequences that have metadata in comments can now be grouped during import
Licensing: Fixed rare error whilst checking Sassafras license
Map to Reference:
Fixed a rare case where Map to Reference introduces a gap 1 bp from the end of the sequence
Fixed references to input reads being discarded sometimes when mapping to a circular reference sequence
Optimize Codons: Fixed a rare crash when running optimize codons on a sequence list
Plugins: Fixed issue where disabling a plugin that another plugin was dependent on caused a failure to start
Plugin Developer Kit:
Added Logs class to allow developers easy access to standard Geneious logs
Fixed a crash when importing multiple files from the wrapper plugin
Public API: Marked deprecated methods
Sequence View:
Fixed a rare case where all annotations may disappear from the sequence view
Save as PDF: Fixed bug on macOS where saving as PDF would send to the local printer
SPAdes: Use python3 by default on MacOS
User Interface:
Cloning reports are no longer light themed when viewing in dark mode
Fixed bug where drag and drop was not showing the correct colors in light mode
Fixed bug where text in the document table could show as multi-line text when the table was resized
Fixed UI error where some annotations were not visible in Text View

New in Geneious Prime 2022.1.1 (Jun 15, 2022)

New in Geneious Prime 2022.1 (Jun 15, 2022)

Features:
Batch Golden Gate: Golden Gate cloning now understands List documents if they contain sequences that are in the same direction
Parts Cloning: Added functionality to support parts cloning, for generating combinations of sequences from existing parts
Primer Import: Updated to import sequences from excel files
Minor Features and Usability Improvements:
Dark Mode: Many small adjustments have been made to improve the user experience
De novo assembly: Improved performance on Geneious de novo assembly, especially on high coverage data sets
Fixes and Minor Changes:
Annotate by Blast: Fixed an occasional crash when running operation on multiple sequences at once
Automatic Update: Fixed a bug where automatic update dialogs were incorrectly presented to the user
BLAST:
Fixed a bug in Custom BLAST where databases with spaces in the name could not get the full sequence
Updated to BLAST+ 2.12.0
Command Line Interface:
Added --multi-file/-m advanced flag to export multiple result documents as individual files
Fixed a bug where CLI was crashing on some headless Linux environments
Fixed irrelevant error messages being occasionally printed
Moved "--include-id" command into advanced help instead of basic help
Back Translate: Fixed a crash when performing this operation on protein lists using "Selected Region"
Dark Mode: Fixed a rare bug on macOS which caused a hang when restarting after switching between themes
Digest into Fragments: Digested annotations are now properly truncated to fragment length with correct intervals
Gateway Cloning: Improved the accuracy of our Att Site Finder and added support for different site variants
Geneious Server: Fixed a rare bug where the progress is not set as complete for finished remote jobs
Import:
Files exported from SnapGene should now have their name imported also, instead of 'Exported'
Fixed a bug importing Newick files containing very deep trees
Merged Paired Reads: Merged output document description mentions how many pairs were merged
Optimize Codons: Fixed bug where some read-only annotations were transferred to the optimized document
Options profiles: Now shows an error message instead of silently failing when an options profile can't be restored
Primers:
Fixed a bug where DNA probe annotations had missing fields
Fixed a bug where edited sequences converted to oligo sequences would not update their melting temperature in the document panel
Fixed a bug where mismatched primers could be merged together in the "Test with Saved Primers" operation
Sequence View:
Fixed a bug where selections were not saved on the source sequence after extracting or translating
Fixed a rare crash when undoing changes to read only annotations
Set Paired Reads: Fixed misleading error message when using this from Workflows on data which can't be paired
Statistics: The length statistic no longer counts gaps and stop codons on protein sequences
Other Notes:
Java: Updated bundled JRE version to 11.0.14+9

New in Geneious Prime 2022.0.2 (Feb 15, 2022)

New in Geneious Prime 2022.0.1 (Nov 17, 2021)

New in Geneious Prime 2022.0 (Nov 17, 2021)

Features:
Annotate by BLAST: Added the option to annotate regions of your sequence using BLAST (option can be found in the Annotate & Predict menu)
Command Line Interface: Released version 2022.0
Dark Mode: Added Dark Mode Beta theme which can be turned on in Preferences
Minor Features and Usability Improvements:
Advanced Preferences: Added filter
Chromatogram Traces: Added option for highlighting regions of traces which do not match base calls
Experimental Features:
Added 'Experimental Features' section to preferences with new functionality for Search Everywhere and filtering while editing annotations
Optimize Codons: Added the option to apply/revert an optimized codon to the annotations context menu
Fixes and Minor Changes:
Alignment View:
Fixed occasional crash when extracting a sequence from an alignment
Characteristics for selection:
Fixed crash when selected primer pairs are facing the same direction
Removed option to test as pair if selected primers face the same direction
Contig View:
Fixed hang selecting a region in the consensus sequence before it has finished calculating
Fixed poor performance on very high coverage contigs
De novo assembly: Fixed rare crash after pressing the 'Stop' button
Document View:
Fixed a rare crash and increased the reliability of selections when switching between different document views
Moved column preferences button to the status bar and redesigned menu layout
Export:
Fixed an occasional crash while exporting csv documents
Fixed a rare issue on Windows where export dialog may hang indefinitely
General:
Fixed bug where documents are sometimes not selected when they should be
Improved detection of faulty hardware and showing a message explaining the problem instead of crashing
Improved detection of local database folder stored within file sync folders
Import:
Fixed a bug when importing tree files with newick format attributes
ZIP file import (containing files of any format supported by Geneious) now also works on files which have had their extension changed from '.zip' to '.geneious' (useful for external software to create files which will be opened in Geneious)
Licensing: Fixed bug where users cannot configure Floating License Manager details in admin properties
Map to reference: Fixed crash in rare cases when a large gap spans the origin of a circular reference sequence
Metadata Importer: Fixed column match not working on alias documents on shared databases
Operating System:
macOS: Fixed a FlexNet group license activation issue if a switched-out-user on the machine has Geneious Prime open in the background
macOS: default_user_preferences.xml can now be loaded from ~/Library/Application Support/Geneious/ directory
macOS: geneious.properties can now be loaded from ~/Library/Application Support/Geneious/ directory
Optimize Codons: Fixed crash when using a space at the end of the forbidden custom motif option
Primer Design: Users are now warned if the primer Dimer Tm is above the Max Dimer Tm limit set in options (caused by an extension)
Search: ‘Include Subfolders’ selection state is now shared between basic and advanced search
Sequence View:
Fixed crash with copying annotation names when duplicate meta data fields are present
Fixed incorrect primer Tm shown in preview box in some cases
Fixed rare crash when using 'Pair Selected Primers'
The ‘add primer annotation’ button will now correctly show up after selection ends are adjusted with the mouse
User Interface: Dropdown arrow added to buttons
Virtual Gel:
Added indication for supercoiled DNA displayed as linear
Fixed crash in print preview dialog and ‘Save to Image’ with a lot of lanes
Other Notes:
Java: Updated bundled JRE version to 11.0.12+7
Java: Geneious and the Plugin Development Kit now use JDK 11

New in Geneious Prime 2021.2.2 (Jul 20, 2021)

New in Geneious Prime 2021.2.1 (Jul 13, 2021)

New in Geneious Prime 2021.2 (Jul 13, 2021)

Features:
Gel:
Improved lane heading usability and displayed enzymes
Allowed fragment view on multiple sequences
Added support for multiple sequences
CRISPR: Displayed CRISPR cut sites for SpCas9 and LbCpf1/AsCpf1 with default PAM sites
Sequence View: Geneious now indicates a premature stop codon on CDS annotations
Annotations: Annotation names and properties can now be batch copied from other annotation, sequence, or document properties
Minor Features and Usability Improvements:
CRISPR: Added support for macOS Big Sur machines by using the latest Python 3.9
De Novo Assembly:
Improved performance and accuracy of Geneious de novo assembler when duplicate reads are present
Upgraded bundled SPAdes version to 3.15.2
Fixes and Minor Changes:
Alignment View:
Fixed out of frame translation in annotation tooltips when annotation starts on a gap
Fixed crash after editing the consensus sequence, then turning off the consensus sequence, then using undo
Fixed crash trying to drag nucleotides around while an operation is running on the alignment
Annotations:
Each row in the annotations table now has a checkbox to make selecting multiple annotations easier
Fixed crash in some situations when selecting many annotations in a long sequence (1 billion bp)
BLAST:
Fixed a rare crash when downloading blast hit results from NCBI
Fixed bug where multi-part databases might be loaded as separate databases into Geneious
Contig View: Fixed crash sometimes when printing or saving an image when the color scheme is "Mapping Quality" or "# of mapped reads"
CRISPR:
Displayed enzyme name on track and tooltip
Fixed Find CRISPR Sites occasionally crashing on sequences with ambiguities
De novo assembly: Fixed crash in rare situations when re-assembling an existing contig
Export:
Added support for exporting sequences within alignments in csv/tsv format
Fixed crash if a document is deleted while exporting or copying the folder which contains the document
Fixed crash when saving some document view's to PDF
File Associations: Associated GenBank .gb, .gbk files with Geneious Prime (for non-MSI installers)
Find Repeats: Fixed occasional crash or incorrect results around the origin of circular sequences
Geneious Server: Fixed bug where Geneious would sometimes incorrectly state "The selected algorithm is not supported in the selected location"
General:
Fixed crash sometimes due to file synchronization software creating conflict files inside a Geneious database
Fixed crash when saving in some situations after copying and pasting sequence fragments within a sequence which is actively linked to other sequences
Fixed rare crash on startup or when creating a new folder on computers with unreliable file systems
Fixed rare crash on startup when a proxy network is configured
Fixed rare hang on startup on some computers
Improved performance of drop down options with lots of values
Prevented crash when data corruption is detected due to a hardware fault and recommend running system hardware tests
Import:
Fixed a crash when importing multiple SAM/BAM/FASTA files together
Fixed crash in some situations when importing a fastq file containing a sequence over 100 Mbp
Fixed crash when importing paired read fastq files when at least one of the files contains no sequence data
Licensing: Fixed bug where sometimes users cannot share group license in the same machine
Map to reference: Fixed crash in rare situations
Mauve Alignment: Fixed crash when Mauve generates an alignment containing invalid nucleotides
Minimap2: Fixed incorrect unused read count in assembly report when not saving the list of unused reads
Operating System:
Fixed crash when macOS Big Sur goes into sleep mode while Geneious Prime is running
Fixed occasional crash when Geneious hangs on macOS Big Sur
Plugins: Improved detection of when problems are due to external plugins and crashes now suggest uninstalling the problematic plugin
Primer Design: Fixed undo/redo shortcut keys crashing "Primer Sequence" field when editing primer annotations
Search:
Fixed rare crash when searching and shutting down Geneious with a shared database connection
Fixed rare crash when searching when the document table is not showing
Sequence View:
Fixed annotation tooltip sometimes disappearing when you try to select text within it
Fixed hang on zero length circular sequences
Fixed crash and/or excessive numbers of dialogs showing when annotating hundreds of sequences with different track names
Fixed crash in rare situation when reverse complementing a sequence
Fixed incorrect translation to Methionine of first codon in annotation tooltips and codon usage statistics when annotation is truncated
Fixed rare crash pairing or unpairing primers on a read-only document
Fixed rare crash when attempting to view some sequences which contain many tracks
Fixed rare crash when filtering annotations
Fixed rare crash when viewing primers with extensions
Fixed translate button crashing or generating a nucleotide sequence when primer pairs are selected
Fixed various rendering bugs when wrapping is on when there are primers with an overhang before the beginning of the sequence
Restriction sites cut position indicators are now larger
Test with Saved Primers: Fixed counter for number of primer results generated
User Interface:
Fixed rare crash when selecting multiple items in the service tree
Fixed miscellaneous bugs
Upgraded to FlatLaf 1.2
Volcano Plot: Fixed a crash when generating a volcano plot with only invalid annotation qualifiers
Workflows: Fixed crash pressing enter in add operation filter when there are no operations matching the filter
Other Notes:
Java: Updated bundled JRE version to 11.0.11+9
Plugin Development:
Added documentation to all database API methods for whether or not they may be called from the Swing thread
Fixed crash in ExampleDocumentViewer when looking at RNA and Protein documents

New in Geneious Prime 2021.1.1 (Mar 16, 2021)

New in Geneious Prime 2021.1 (Mar 16, 2021)

Features:
Filter: Re-introduced filter functionality to the document table
Sequence View:
Added option to show amino acid numbering to the translation options
Can adjust the bounds of a selected region within a single sequence by dragging the ends of a selection
Statistics: Added A[280] of 1mg/ml correction factor to protein and nucleotide translation statistics
Minor Features and Usability Improvements:
Geneious Server Database: requireUnixAccounts property added to allow users to log in without Unix account on server
Shared Database: Added 'database-port' property to geneious.properties to configure port, when database uses a port other than the default one
Search: Re-designed basic search
Update Process: Improved update speed on Windows and Linux
Workflows:
Editing is now non-modal so it is easier to test workflows without closing and reopening them
Automatic export now includes dependent workflows
Added new menu item for running custom Java code
Custom Java code has new simpler entry points for common sequence editing tasks and shows line numbers
Fixes and Minor Changes:
Augustus Plugin: Fixed problem preventing it from working in Geneious Prime 2021
Export and folder copy: When some documents can't be accessed, can now optionally continue exporting the accessible documents
File Import: Files imported from a zip archive now have the original zip file as their "imported from" source
GenBank Import/Export: Fix to ignore importing/exporting the direction of single point annotations
Geneious Cloud Plugin: No longer bundled with Geneious
General: Fixed bug on systems with multiple screens on Windows where sometimes the main Geneious window would not appear when starting Geneious
Import: Fixed dragging and dropping files into folders not working without first clicking on the folder tree
Local BLAST: Default blast updated to the latest version
Mauve Alignment: Prevented creating or viewing of invalid alignments
ORF Finder: Fix double annotations generated over the same interval on different reading frames
Primer Design: Fixed crash in "Primer Sequence" field when editing bases
SAM/BAM Import: Fixed crash when importing when out of disk space
Search: Fixed poor performance when selecting which field to search for from the drop down list
Sequences: Fixed some cases where copy pasting a sequence selection into a text editor would copy paste an entire document
Sequence View: Fixed annotation popup dismissing occasionally as you move the mouse towards it to select and copy the contents
Sequence View: Fixed crash when protein sequences contain restriction site annotations
Sequence View: Fixed incorrect ORF finder results after changing whether a sequence is circular
Sequence View: Fixed rare crash when editing annotations
Sequence View: Fixed sequence names being drawn unnecessarily truncated sometimes
Sequence View: Improved performance adding primer extension restriction sites and when working with large lists of genomic sized sequence
Spreadsheet Import: Fixed a bug when importing documents with a topology field
Text View: Clicking "Copy Full Sequence" button should no longer occasionally cause crashes
Text Viewer: Fixed rare crash when using text viewer on large PDB data
VNTI/Rebase Importer: Fix occasional crash when importing VNTI database or enzyme documents before Geneious' internal enzyme list is initialised
Operating System:
macOS: Fixed GateKeeper warning "Geneious Prime.app can't be opened because Apple cannot check it for malicious software" on M1 devices
macOS: Fixed Geneious Prime constantly crashing after system restart on Big Sur due to max memory changes in Info.plist
macOS: Max memory settings is now set in '~/Library/Preferences/Geneious.in.use.vmoptions' rather than editing Application 'Info.plist'
Other Notes:
Plugin Development: Fixed wrapper plugin crash when using the 'write each input sequence to a separate file' setting on alignments

New in Geneious Prime 2021.0.3 (Dec 24, 2020)

New in Geneious Prime 2021.0.2 (Dec 24, 2020)

New in Geneious Prime 2021.0.1 (Dec 2, 2020)

New in Geneious Prime 2021.0 (Dec 2, 2020)

Features:
Sequence View: Added options to highlight restriction sites affected by Dam, Dcm, or EcoKI methylation
Statistics: Most Sequence View statistics are now available as fields in the document table
CRISPR: New scoring strategy for on-target activity, proposed by Doench et al 2016
User Interface:
Redesigned user interface for Geneious Prime
Changed Geneious default font to Noto Sans
Updated icons
Minor Features and Usability Improvements:
Geneious Update: Streamlined the updating experience
Genetic codes: Added new genetic codes available on the NCBI list
GenBank Import: Added support for importing metadata from comments
Restriction Cloning: Labels for selected restriction sites made more obvious
Shared Database Documents: Shareable links enabled on shared document/s by accessing right click menu item “Copy Document Link”
Menus:
Add and Export menu buttons added to main toolbar
Contact Us button moved to Help menu button in the toolbar
Back Up button moved to Export menu button in the main toolbar
Fixes and Minor Changes:
Alignment View: Fixed rare crash when extracting an alignment from an alignment
Apply Variants to Reference Sequence: Fixed crash when reference sequence has an insertion variant on the end of it
Batch rename: Fixed bug when used from workflows where some fields were not available to use as a source for building the new value of the field to rename
Cloning: Primer characteristics now include the extension
Contact Support: Fixed a bug where our feedback server was occasionally unavailable
General: Fixed memory leak which caused Geneious to use an extra 1 MB of memory for every 100 documents previously viewed until Geneious is restarted
General: Improved performance when working with thousands of selected documents
Identify Organism Workflow: Now supports running on protein sequences
Import/Export: Updated Genbank annotations
Local Blast: Fixed a bug which was causing tracks to be hidden in local blast results
Metadata Importer: Fixed crash while preview is being generated
Metadata Importer: No longer showing "failed to use some potential references" dialog when no documents match
NCBI BLAST: Updated BLAST to use the latest NCBI limitations
Operating System: Fixed crash when MacOS11 goes into sleep mode while Geneious Prime is running
Plugin Installation: Fixed failure to install plugins if # is part of the operating system user name
Primers: Fixed crash when placing primer pairs at the origin of a circular sequence
Restriction Enzymes: Improved handling of duplicated enzymes
Search: Improved performance when searching local documents
Search: "This Folder" no longer shown as an option in search when the selected service is not a database folder
Sequence View: Added an 'Edit: ' prefix to the automatically created Insertion, Deletion, and Replacement annotation types
Sequence View: Fixed crash occasionally when using "Circular Overview"
Sequence View: Fixed crash when cancelling Annotate & Predict operations on large data sets with unsaved changes
Sequence View: Fixed crash when foreground and background residue colors are very similar
Sequence View: Fixed primers overhanging the end of the sequence sometimes causing it to start at 0% zoom and the zoom in button not working
Sequence View: Fixed rare crash when changing between sequences in the sequence viewer
Sequence View: Scrolling an entire page at a time now has a very small overlap with the previous page
Shared Database: Added MS SQL Server support for Named Instances in the host name
Shared Database: Disconnecting from a shared database no longer leaves hanging connections
Tree View: Fixed rare crash when displaying large files
VNTI GenBank Importer: No longer overwrites feature annotations with comment annotations
Other Notes:
Java Version: Updated bundled JRE to 11.0.9

New in Geneious Prime 2020.2.4 (Sep 17, 2020)

New in Geneious Prime 2020.2.3 (Aug 25, 2020)

New in Geneious Prime 2020.2.1 (Jul 15, 2020)

New in Geneious Prime 2020.2 (Jul 15, 2020)

Features:
New tool to Analyze CRISPR Editing Results
Align and cluster NGS sequencing reads from the results of a CRISPR editing experiment
Supports a variety of applications including HDR, NHEJ and base editors
Visualize variants compared to the unmutated reference sequence
Analyze the frequency of variants and their protein effects
Enhanced Search Interface
Search folders and documents from a single unified interface using text queries in real time
New functionality to search for analysis tools (Actions) available within Geneious Prime
Easily access additional advanced search options
Quick access to recently viewed folders and documents
Codon Optimisation Improvements
Informative tooltips on Optimized Codon annotations give information about synonymous codons and their frequencies in the chosen codon usage table
Annotation properties including directionality and CDS codon_start information are now taken into account when optimizing regions chosen by selecting annotations
When optimizing a selected annotation with multiple intervals, the selection is optimized across intervals and codons are allowed to span adjacent intervals
When optimizing a reverse-directed selected region, the reverse complement sequence is now optimized
Minor Features and Usability Improvements:
Document Lineage: Maintain active links between documents when adding, editing or deleting annotations on child documents
Back and Forward Buttons
History is persistent between Geneious sessions
Use shift click to go back and forward between folders instead of documents
Annotation Tracks
Annotations in tracks now include a link to track properties in the annotation tooltip
Heatmap color schemes can now be customized
Set default translation frame settings for all documents in Sequence View
Virtual Gel: Can now rearrange lane order on the gel by dragging
Import protein sequences in SnapGene .prot file format
Restriction Cloning Usability Improvements
Default fragment selection for backbone sequences improved, including selection of the larger fragment and avoiding internal cut sites
Enhanced visual indication of the sequence fragment which is selected for cloning in the preview panel
Automatic selection of compatible enzymes when adding new inserts to reaction improved
Sequence length for cloning operations now limited to a maximum of 100kb - limit can be adjusted in advanced preferences by changing Cloning.maximumAcceptedSequenceLength
NCBI database searches for text queries and NCBI BLAST can now be enabled/disabled independently of each other
Improved accuracy of consensus calling in the presence of Sanger heterozygotes
Fixes and Minor Changes:
Align/Assemble
Map to Reference: Unused reads document produced include the 'Sample' field that was previously only present on the contigs produced
Minimap2: Fixed crash when using assemble by name
Fixed Assemble by Name to store a link from the contigs produced to the reference sequence source
Clustal Omega: Fixed crash when using this after manually editing the 'Command Line' meta-data type
Annotate and Predict Menu: changed the ordering of menu items to be grouped more logically
Back Translate: Fixed a bug where annotations could appear in the wrong place when back translating a selected region of a protein
BBTools: Updated to version 38.84
BLAST and NCBI Search
Fixed a rare crash which occurred sometimes when BLAST searching on a local database with long file names
Fixed crash or corrupted query centric alignment when copying BLAST results into folders containing other BLAST results
Updated to display correct values for hit tables when tblastn(AA query,DNA database) against a database which is results of a blast
Fixed bug where tblastn results sometimes had the Molecule Type field set to DNA for pairwise amino acid alignment results
Prevent searching NCBI for empty accession numbers
Chromatogram Sequences: Fixed incorrect rendering when mapped to long (million bp +) reference sequences
Command line tools: Fixed reported output from command line tools (e.g. Flye) containing a duplicated section of text occasionally
Expression Analysis:
Fixed failure to install DESeq2 on some Windows machines due to interference from virus scanner
Prevent crash in Volcano Plots when an annotation doesn't have a name
Import/Export
Genbank Export: Now exclude restriction sites from the exported list of features
Genbank Import: Fixed typo in VNTI Genbank format import feature key - feature type 29 will now import as annotations of type ‘promoter eukaryotic’ instead of ‘promoter uukaryotic'
Genbank Import: Fixed hang when importing Genbank files containing large COMMENT sections
Genbank Import: Primer extensions and mismatch information are now imported correctly from SnapGene Genbank format files (.gbk)
SnapGene .dna file import: Invalid nucleotide characters in primer sequences will now cause import to fail gracefully with a useful error message
Spreadsheet Sequence Import: Now prevents primer import if primer extension data contains invalid residues
SAM/BAM Import: Sample name is now imported as the 'Sample' field in Geneious so that variant calling and expression analysis work correctly on mappings with multiple reference sequences
SAM/BAM Import: Fixed crash when importing SAM/BAM files which reference sequences names that don't belong in any sequence lists in the folder imported into
Multi file Import: Fixed a bug which would cause crashes in some cases when trying to import multiple files of different types in bulk, for example a .caf file with another file
Genbank Submission: Fixed "citation date is in future" error when submitting to Genbank sufficiently early in the day in time zones ahead of GMT.
Metadata: Fixed hang or poor performance when selecting a sequence, during shutdown, or during Genbank export when large meta data fields are present on a sequence
ORF Finder:
‘Continue outside sequence’ fixed to begin ORF annotations outside the sequence where appropriate
Fixed ‘Continue outside sequence’ generating erroneous ORF annotations with internal stop codons
Primer Design: Fixed occasional crash with long paired primers on circular sequences
Restriction Enzymes: Prevent crash during Geneious startup when an invalid enzyme file is being loaded
Search: Updated advance search to allow searching for custom boolean fields
Sequence View
Now uses 3D structure annotation images (alpha helix, beta sheet) for Uniprot files like it previously only did for Genbank files
Fixed sequence viewer switching to low quality rendering after dragging a track
Fixed extracting a track annotation as an active link causing the annotation to become duplicated
When showing the translation for overlapping ORF/CDS annotations which have different frames, it now uses the translation frame of the selected annotation.
Fixed crash sometimes after editing the same sequence prior to saving changes from two different windows.
Fixed crash if advanced preference SequenceViewer.maximumZoomOrScrollAnimationDuration is set to 0
Text View
It is now possible to display metadata fields in Genbank format
Non-default Genbank display options are now applied properly when copying to the clipboard or saving as play text
Fixed bug where changes to the display options didn't take effect when ‘OK’ was pressed when displaying Genbank format
Fixed a bug where sequence documents with HTML tags in the name or description fields weren't displayed completely
General
Startup performance when local documents contains thousands of folders improved
Fixed memory leak which caused Geneious to use an extra 1 MB of memory for every 100 documents previously viewed until Geneious is restarted
Fixed crash when attempting to rename a folder after deleting it
Fixed crash which occurred occasionally when shutting down Geneious
Wrapper Plugins
Fixed errors attempting to run some wrapper plugins such as Clustal Omega and Flye when Geneious Prime was installed as root on Linux
Fixed crash if the wrapped program is not bundled with the Geneious plugin
DevKit: Fix crash in ExampleDocumentViewer when viewing non nucleotide sequence documents
Public API: Added a new method to get all the divider locations in a main menu
Shared Databases:
Oracle 19c is now supported
Added compatibility with MySQL 8 using the included MySQL Java Connector/8.0 which is compatible with MySQL 5.6 and higher. Current users of MySQL Java Connector/5.1 will need to set the Driver Class name in their connection settings to com.mysql.jdbc.Driver
Fixed error initializing an empty MySQL shared database when using a recent version of MySQL Java connector
Fixed issue whereby a user specified Postgres jdbc jar was ignored
Fixed issue when using Postgres version 9 or greater that was not deleting disk files containing data for large documents that were deleted from the database, allowing orphaned files to accumulate in the user's directory. These files will now be deleted in the background when Geneious Prime is running
Fixed problem scheduling background cleanup processes when MySQL or SQL Server database is in different timezone than Geneious client
Fixed crash and/or hang when changing Geneious data location sometimes while connected to a shared database
Geneious Server:
Fixed problem running jobs submitted by Geneious Prime on Linux when the user home directory is network shared with the computing cluster

New in Geneious Prime 2020.1.2 (Apr 7, 2020)

New in Geneious Prime 11.1.5 (Jul 17, 2018)

New in Geneious Prime 11.1.4 (May 1, 2018)

New in Geneious Prime 11.1.3 (May 1, 2018)

New in Geneious Prime 11.1.2 (Mar 6, 2018)

New in Geneious Prime 11.1.1 (Mar 6, 2018)

New in Geneious Prime 11.0.5 (Jan 31, 2018)

New in Geneious Prime 11.0.4 (Jan 9, 2018)

New in Geneious Prime 11.0.3 (Oct 31, 2017)

New in Geneious Prime 11.0.2 (Oct 3, 2017)

New in Geneious Prime 11.0.1 (Oct 3, 2017)

Bugs Fixes and Minor Changes:
Cloning: Optimize Codons operation has move from the Annotate & Predict menu to the Cloning menu
Plugins: List of installed plugins is now sorted by description by default
Batch Export: Fixed crash attempting to batch export to a Geneious format version that is not supported by the all of the documents
BLAST: Fixed crash sometimes when running BLAST on an alias to a deleted document
Assembly: Fixed bug causing assembly to unselect the document you are viewing while assemble by list is running in the background
Assembly: Fixed duplicate contig names when assembling by sequence list
Assembly: Fixed very poor performance in rare situations in the Geneious de novo assembler
Assembly: When assembling each list separately, if one set produces an error it no longer stops assembly of all other sets from running
Map to reference: Changed 'only map paired reads which map nearby' to require them to be within insertSize±insertSize*2 and introduced 'which map closely nearby' option for the old behaviour of insertSize±insertSize/2
Workflows: Added option to record the author of a workflow
Workflows: Added option to 'Randomly Sample Sequences' workflow to use the first N sequences from the source list (faster than randomly sampling)
Shared database: Fixed poor startup performance of Geneious sometimes when auto-connecting to a shared database
Shared database: Fixed crash in change group of folder when user's private group is the only one in which they have sufficient rights
Shared database: Fixed occasional failure to prevent creation of group with duplicate name, empty string, or with leading or trailing space
Sequence Viewer: Fixed so that 'save as image' does not scroll to the start of the sequence
GenBank Importer: Fixed a bug importing flat files where a space was required in DBLINK entries before the accession number (now files with and without the space will import)
GFF Exporter: Exports sequences in fasta-format at bottom of the file and does not export all-blank sequences
PCA Plots: Fixed label positioning bug
Volcano Plots: Fixed crash selecting annotations before viewing plot
SPAdes: Fixed failure on paired reads that use .1 and .2 instead of the more usual /1 and /2 suffix
Find CRISPR Sites: Fixed a warning label that was showing up when it did not need to
Sequence Extraction: Fixed a bug where annotations spanning the origin were split into two intervals when reverse complementing a whole circular sequence, and primers spanning the origin were deleted
Analyze Silent Mutations: Fixed handling of circular sequences, truncated annotations, and potential restriction sites extending past the final codon
General: Fix memory leak (and potentially later crash) when deleting a document that is open in a new window

New in Geneious Prime 11.0.0 (Oct 3, 2017)

FEATURES:
Analyze Silent Mutations - Annotate potential restriction sites that can be introduced by silent mutations
Volcano Plots - Visualize gene expression in an interactive view that synchronizes your selection with the Annotations and Sequence View
Cloning: Create an empty enzyme set via File > New and add enzymes to it
PCA Plots: Improved label positioning and added a legend
Sequence/Alignment View: Selections of multiple annotations are now synchronized with the Annotations view
Sequence/Alignment View: Added annotation filter 'truncated' term which matches annotations with a truncated interval
Workflows: Added 'Group sequences by name' workflow for grouping sequences with the same name prefix into a list
CSV/TSV Exporter: Now supports exporting in the compressed .csv.zip and .tsv.zip formats
Better Fastq Import:
Paired reads can now be associated with each other during import and Genieous will do it's best to guess how they're paired
Read technology can also be set during import (read technology is used by some assemblers)
CRISPR Improvements:
Added support for Cpf1 enzyme variant with 5' PAM site
Added 'Target Sequence' as a qualifier on CRISPR annotations
BUGS FIXES AND MINOR CHANGES:
BBTools: Upgraded to version 37.28
Sequence View: When shift-clicking in circular sequences, the selection is now always made clockwise around the circular instead of selecting the shortest selection
Sequence View: In wrapped mode, improved performance and fixed transient rendering glitches when scrolling
Sequence View: Fixed annotating different length sequences with a truncated annotation to keep the truncated status on all sequences
Sequence/Alignment View: Stopped editing mode getting turned on automatically in some situations where it was unnecessary
Sequence/Alignment View: 'Create separate annotation for each interval' option now remembers whether it was previously on or not
Sequence/Alignment View: Fixed crash sometimes when showing annotation results in a separate window
Sequence/Alignment View: Fixed bug where annotation type occasionally remained off in the controls after an annotation of a new type was added
Sequence/Alignment View: Fixed a rare crash that can occasionally happen after saving a large document
Alignment View: Fixed crash sometimes when reverse complementing a circular alignment
Alignment View: Improved performance when zoomed out while showing translation
Alignment View: Improved performance when running 'Live Annotate and Predict' on alignments
Alignment View: Fixed annotations spanning the origin of the consensus sequence not being fully rendered
Alignment: Fixed incorrect default parameter values for MUSCLE
Transfer Annotations: Fixed transfer of annotations spanning the origin in circular alignments
Translation: Added 'Remove final stop codon' option to translation from sequence view
Translation: Fixed bug turning off 'Remove final stop codon' option would not work on some sequences in workflows
Backup: Now remembers the last backup location you used, separately from other export operations
NCBI Search: prevents duplicate download of full documents and fixed possible endless loop when failing to download
NCBI Search: Fixed crash in some instances when Gene documents don't have a commentary section
NCBI Search: Added 'Targeted Loci' rRNA databases
SPAdes de novo assembly: Fixed a fresh install not working on recent versions of Windows
Import: Fixed crash when importing multiple files when out of disk space
Genbank Import: Correctly imports all sequences from gb files where some sequences end with a single CONTIG line
Genbank Export: Fixed crash for some files that don't have an accession
Genbank Text View: Shows Genbank entries in strict format
Workflows: Fixed crash when a workflow exposes the alignment automatically determine direction setting and the workflow is then used on protein sequences
Sequence Extraction: When extracting using the annotations table without concatenating intervals, multi-interval annotations are now truncated (affects interval indices in result)
Reverse Complement: Fixed crash extracting reverse complement sequence list from medium-size contigs (> 10,000 sequences)
Start up on Windows: Fixed rare crash on start up
Shutdown: Fixed hang on shutdown when there is a very large tree document in your database
Expression Analysis: Added option to calculate expression levels for miRNA, ncRNA, or any annotation type that ends with RNA
Compare Expression Levels (Geneious method): Fixed weirdly formatted p-values like 0E-39 which should be 0
Compare Expression Levels (Geneious method) and Calculate Expression Levels: Values produced now have 2dp instead of 1dp accuracy
Compare Expression Levels (DESeq2 method): Confidence and absolute confidence are now derived from adjusted p-values
PDF Documents: Fixed crash in some situations after importing a PDF document into Geneious
Annotate from Database & Test with saved primers: Primer annotations that have identical binding site and extension are now merged
Primer Annotations: Primers with an extension are now visually different
Document Table: "Modified" date column is now displayed by default
Exporting Tables: better default names when exporting Annotation or Restriction Fragment tables
Tadpole de novo assembly: If Tadpole produces no contigs, all messages produced by Tadpole are now included in message displayed in Geneious
Map to reference / de novo assembly: Algorithm names displayed in most locations are now shorter. e.g. replaced "Bowtie2 - Fast and accurate read mapper" with "Bowtie2"
De novo assembly: Added option to specify the minimum number of sequences a contig must contain before it may be circularized (previously this was always 3)
GFF Import: Fixed crash when importing into a folder containing an alias document
Preferences: Fixed duplicate entries appearing in the "save selected documents" drop down list
Performance: Fixed occasional half second pauses in Geneious when showing some dialog windows
EMBOSS tools: Fix an error when searching for some long motifs
MacOS installation: Fixed problem running certain bundled plugins when user does not have write access to the install directory
Chimera Filtering: Update Cygwin DLL bundled with Windows version to 2.8.2 to satisfy security scans even though vulnerability did not affect Geneious
Geneious Server Database/Shared Database: Fixed a crash that occurs when importing SAM/BAM files and trying to use a reference from the same folder
Security: Geneious now uses any CA trusted root certificates installed in the OS for SSL connections
Security: New Advanced Preferences option SSL.CustomTrustedCertificates allows storing one or more custom trusted CA root certificates for SSL connections
General: Fix incorrect warning when running under CentOS 7
PLUGIN DEVELOPMENT:
Exposed option for choosing colors (Options.addColorChooserOption)
Added method for adding help button next to an option (Option.setHelp)
Added methods to access selected annotations from annotation generators via SequenceAnnotationGenerator.SelectionRange
Added method to access the Java binary used by Geneious at runtime (SystemUtilities.getJavaExecutable)
GENEIOUS SERVER AND GENEIOUS DATABASE SERVER:
Add support for installation on version 7.x of Red Hat Enterprise Linux (RHEL) and CentOS
Update to version 7 of Tomcat
Removed login option to accept untrusted certificates, superseded by SSL certificate related changes in Geneious
Add support for clusters that do not report status of jobs that have been completed, such as is the default for Univa

New in Geneious Prime 10.2.3 (Jul 11, 2017)

Bugs Fixes and Minor Changes:
Optimize Codons: Restriction site annotations will now be recalculated instead of being copied across, which could previously introduce errors
Geneious Server Database/Shared Database: Stop showing a message dialog each time the server is disconnected
Geneious Server Database/Shared Database: When changing the group of a folder, the apply to subfolders option is now off by default
Geneious Server Database/Shared Database: Admin group role now required to change folder groups (except with Geneious Server Database connection and setting for "All users" can manage groups)
Geneious Server Database/Shared Database: Fix error when adding new user with primary group of User Private with external authentication
Geneious Server Database/Shared Database: Remove restriction that a folder can have Private group only if all folders in its tree do
Geneious Server Database/Shared Database: Make browsing folder in large database much faster than 10.1
Geneious Server Database/Shared Database: Fix problem that caused 'doesn't contains' searches to return the wrong results
Geneious Server: Fix Univec BLAST database used for trimming
Icons: Shared folders will now have an icon overlay the same colour as their default colour on every distribution
Generate or Extract Consensus Sequence: The Ambiguities field is no longer copied to the full or partial consensus sequence since it could be incorrect if only a partial sequence is extracted. This field is still automatically calculated on full or partial sequence extractions with quality information
FastQ Export: Spaces in sequence names are no longer replaced with underscores by default; this can be changed by setting an advanced preference
Copy Translation: Fixed crash copying translation from selected truncated annotation
SAM/BAM Import: Fixed crash in rare situations when important SAM/BAM files
General: Fixed bug where operations sometimes deleted all annotations from source document
UniVec: Updated the bundled UniVec database to the latest version
Import: GenBank Flat format importer now recognizes file with .seq extension
Import: Sets correct dates for VectorNTI files that previously showed dates before 1995
Import: Multi-Interval annotations in Genbank files exported by VectorNTI are imported to the correct location
Import/Export/Backup: Fixed Geneious suddenly exiting during import/export under Windows 10 Creators Update when GodMode is enabled
NCBI Blast: Fixed crash when running blastx with a query that has editing annotations that need to be reverted
General: Fixed crash in some situations when out of disk space

New in Geneious Prime 10.2.2 (Jun 6, 2017)

New in Geneious Prime 10.2.1 (Jun 6, 2017)

Bugs Fixes and Minor Changes:
Tree Building: Fixed crash with third-party tree builders that don't provide any user-defined options
BLAST from workflows: Fixed bug where it would use the default database instead of the selected database when run on a nucleotide sequence list
Alignment Extraction: Fixed out-of-frame inline translation on alignments extracted from alignments when the extraction starts with an internal gap
Workflows: Fixed bug where adding a new step would sometimes add it to the end of the workflow instead of after the currently selected step
Sequence Editing: When deleting nucleotides from the start of a CDS annotation, the codon_start property is automatically adjusted to keep the translation of the remaining section of the annotation the same as it was previously
Alignment/Contig View: Annotation tooltip 'Length' field has been renamed to 'Length (with gaps)' and a new 'Length' field introduced which contains the ungapped length
Save as Image: Fixed sequence numbering getting slightly clipped sometimes on the right hand side of the image
Restriction Cloning: Fixed bug where Workflows always used Enzyme Set instead of Annotated Enzymes, or where it couldn't be selected if the initial document didn't have annotated enzymes
Restriction Cloning: Fixed poor performance when digesting large sequences into fragments
Document Searching: Track names and properties on newly created or edited sequences are now indexed for searching in local and shared databases
Document Searching: Improved speed for searches on large shared database
Nexus Tree Importer: Internal node attributes can now be specified as branch support values or node labels and will behave appropriately when rerooting
CSV Exporter: Better handling of descriptions that contain elements that look similar to html < tags /> but aren't
De novo assembly: Fixed crash when using Windows 10 Insider Preview
De novo assembly: Fixed crash in rare situations when the 'circularize contigs' and 'produce scaffolds' settings are both on (they are both on by default)
Start up: Fixed crash on startup in rare situations on Windows
NCBI Search: Fixed cases where summary documents were shown multiple times if connection was interrupted while the search was running
Find Variants/SNPs: Fixed crash when setting strand-bias threshold to 50% when reads contain ambiguities
NCBI Download: Fixed bug where genome summaries were not replaced by the full downloaded document if the summaries don't have a version number
Printing/Saving As Image: Fixed bug where saving an image of an entire circular sequence while zoomed in would omit annotations outside the viewed region
Find Heterozygotes: Fixed bug where no heterozygotes were found if only the left-hand end of the sequence was annotated as trimmed
Genbank Document Exporter: When exporting strict Genbank format, annotation names are now saved as 'standard_name' qualifiers
BBTools: Upgraded to version 37.25
Sequence Extraction: When extracting a primer or probe from a sequence list the resulting document is now of type Oligonucleotide
Optimize Codon Usage: Fixed bug running from Workflows where result sequence was identical to input
Plugin Development:
Added new method DatabaseService.showAdvancedSearchByDefault to allow a database to show advanced search by defaults instead of basic
Added new Options.addChildOptions() method that allows child options to stretch vertically
Public API: Parameter names are no longer obfuscated
Geneious Server:
Fixed a bug where the new database administrator settings introduced in 10.2 were not initialized correctly and displayed the wrong values for new databases
Fixed a bug where multiple dialogs would be displayed when user was disconnected
Fixed various other bugs related to new settings introduced in 10.2

New in Geneious Prime 10.2 (Jun 6, 2017)

FEATURES:
Compare Expression Levels: PCA plots for multi-sample RNA-seq data
Workflows: Added support for cloning operations
BUGS FIXES AND MINOR CHANGES:
Workflows: Added buttons to allow reordering of workflow steps
Workflows: When run on operations that generate annotations on a referenced sequence in an alignment/contig (e.g. Find Variants/SNPs) added an advanced option for whether to propagate the annotations back to the referenced sequence
Workflows: Replaced 'Truncate Annotations' workflow with 'Modify Annotation Intervals' workflow that also allows extending or shrinking annotation intervals
Workflows: When an operation in a workflow saves documents to a sub-folder, those documents are now passed on to the next step in the workflow
Sequence View: On multiple unaligned sequences, the little previous and next buttons for each annotation type now work
Sequence View: Added "Don't show again" option to the message about there being too many annotation or track types to show them all in the controls
Annotations Table: Order of columns can now be set under "Manage Columns"
Document Table: Order of columns can now be set under "Manage Columns"
Folders: Added "Collapse All" and "Expand All" options to right-click menu on folders that have subfolders
Folders: Geneious now uses an icon to indicate if a folder is shared with other users, includes folders in a Shared Database or Geneious Server Database
Shared Database: Folders created under the root folder will now always be created in a user's primary group
Shared Database: Folders that are not created under the root folder will now always inherit the group of their parent folder
Shared Database: Fixed a problem that prevented editing of group roles when using Oracle databases
BBTools: Upgraded to version 37.17
Map to reference: Improved alignment around gaps near ambiguity characters
Map to reference: Fixed crash using "Assemble each list separately" when one of the lists contains no sequences
Map to reference: Fixed bug where deletions of repeat regions over 15bp were not being discovered
Map to reference: Fixed out of memory error when mapping reads (that should fail to map due to exceeding the maximum number of mismatches allowed) spanning the origin of a circular reference sequence
Assembly / Map to reference: output contigs and consensus sequences record the algorithm used in the document description
SPAdes assembler: Fixed so that if you are using an unsupported version of Windows, you can still run SPAdes on Geneious Server
SPAdes assembler: The trusted and untrusted contigs options no longer default to the same trusted/untrusted contigs as you used for the previous assembly
Contig View: Added option to sort reads by the number of differences from the reference sequence on contigs with fewer than 10,000 reads
Sequence Extraction: Fixed crash extracting a region while also viewing an empty sequence
Sequence Extraction and Merging Paired Reads: The 'Read Technology' field (and other fields) are copied to the derived documents
Sequence Extraction and Translation: Fixed bug where translations were wrong after extracting a partial annotation on a circular sequence
Copy Translation: Fixed crash copying from a circular sequence when the first codon spans the origin
Alignment: Fixed crash sometimes when aligning after reverse complementing a sequence containing a mixture of DNA and RNA
Alignment: Fixed crash when running MUSCLE on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)
Alignment: Fixed crash when running MAFFT on sequences containing inosine with "Automatically determine sequences' direction" turned on
Gibson Assembly: If sequences are compatible it doesn't create primers and doesn't warn about filled in overhangs
Gibson Assembly: RNA sequences used to create an invalid warning in the report about the reverse primer binding at multiple locations
Cloning: Fixed crash when existing overhang annotations were adjacent to a cut site or PCR
Cloning: Display warnings if similarity of overhangs is above threshold
Gateway Cloning now records the used intervals and shows them in the lineage
Lineage: Fixed incorrect interval when extracting a region across the origin from a circular sequence while viewing multiple sequences
Primer Annotations: Fixed crash when trying to create a primer from an annotation that is between two bases
Compare Expression Levels: Fixed crash that would occur when DESeq2 received a count table containing at lease one zero per gene
Compare expression levels: Fixed crash when using Geneious method on multiple reference sequences when the first reference sequence does not contain both tracks
SAM/BAM Export: Improved performance on data with high coverage paired reads (2 to 3 times faster)
Tree Building: Fixed crash that could occur when building trees out of alignments backed by Genbank documents in some tree builders
Tree Building: Fixed crash that could occur when cancelling a tree building operation on unaligned sequences
Tree Viewer: Fixed missing attributes from "Show branch labels"
3D Structure viewer: Fixed background CPU usage sometimes after closing a view that was using the 'Spin' effect
Data Location: Fixed crash after moving your Geneious data to a location that Geneious is unable to properly access (e.g. due to free low disk space)
Repeat Finder: Fixed crash when finding repeats in the selected region only when the selected region spans the origin of a circular sequence
Apply Variants to Reference Sequence: Fixed crash when running it on a sequence without variant tracks
Find Variations/SNPs: Fixed incorrect protein effect for some start codon variants that would translate as M in a start codon but would translate differently at other positions (e.g. CTG translates as M as a start codon, but L elsewhere)
Find Variations/SNPs: 'Protein Effect' field now says 'Start Codon Loss' if the start codon translation changes from M to a different amino acid
Wrapper Plugins (e.g. RAxML, FastTree, Garli): When saving terminal output that is too long, the text will be truncated such that the first and last 500 lines are always retained
Newick Tree Export: Fixed bug where exporting MrBayes trees with support values failed to save support values
Document Notes: When text is too long to display in the "Info" tab, the text will be truncated such that the last 1000 characters are still shown
Printing: Fixed hang that could happen when printing documents as images or PDFs
General: Fixed crash sometimes when double clicking menu items
General: Gracefully fail instead of crashing when Geneious data is in a Jottacloud synced folder which creates conflicting synchronization files
GENEIOUS SERVER:
Automatic creation of a private folder group for each user
"Show Inaccessible Folders" option is no longer available for Geneious Server Database
Logging of events that affect user access to documents
New database administrator settings. These are enabled for new databases, disabled for existing ones and can be changed at any time:
Assign new folders under the root folder to the user's private group instead of the user's primary group
Allow regular i.e. non-admin users to create and change the group of folders themselves
Prevent users from storing new documents in the root folder

New in Geneious Prime 10.1.3 (Mar 21, 2017)

Bugs Fixes and Minor Changes:
General: Fixed a crash that would occur when changing displays in Linux
General: Fixed a rare crash that could occur on startup
CRISPR: Put the PAM sequence in the annotation so that it can be used for filtering
CRISPR: Got around crash that could happen when discovering CRISPR sites with high levels of ambiguity
De Novo Assembly: The limit for the maximum contigs saved can now be set as low as 1 (previously 100 was as low as it could be set)
De Novo Assembly: Fixed a crash on some non-English language versions of Windows
Find Restriction Sites: 'Must cut between' now finds enzymes that cut outside their recognition sequence if the region was limited to exactly the cut region
Gibson Assembly: Improved handling of already compatible overhangs and Gibson Primer Extension annotations
Golden Gate: Fixed incorrect lineage interval for circular documents when no PCR required and selected region crosses the origin
Map to reference: Fixed occasional crash (or minor mis-alignment of reads around insertions) when structural variant discovery is on
NCBI: A full accession which includes the version is now included in the Accession field
NCBI: Fixed a bug that could cause the download of an out of date version of a sequence when using an old summary document. Now downloads the most recent version
Primers: Fixed incorrect GC content and other Document Table fields on primers extracted from a sequence list using Convert to Oligo
Printing: Fixed an issue where lines were occasionally skipped when printing text views, including Assembly Reports
Restriction Cloning: The ends of linear constructs can now be digested back to any selectable restriction site
Restriction Cloning: Fixed crash for when propagating changes if enzymes could cut directly next to each other
RNA seq expression analysis: Disabled libraries installed by another program from being used by Geneious on Windows and Mac
RNA seq expression analysis: Fixed a bug where tracks with no condition were being considered a third condition
Sequence/Alignment View: Fixed pressing enter in filter text not jumping to correct annotations if enter was pressed earlier while filtering was still in progress
Sequence/Alignment View: Fixed crash when saving after adding annotations to the consensus sequence of a blastx result
Sequence/Alignment View: No longer shows the track tooltip when over the track drop down menu
Tree Viewer: External nodes are now correctly highlighted when hovering over their labels in zoomed in views
Trim Ends on alignments: Fixed hang when choosing the option to remove trimmed regions (instead of annotating them)
Workflows / Licensing: Fixed a crash that would sometimes occur after viewing workflows and then deactivating your license

New in Geneious Prime 10.1.2 (Mar 7, 2017)

New in Geneious Prime 10.1.1 (Mar 7, 2017)

Bugs Fixes and Minor Changes:
NCBI: Uses Accession.Version numbers rather than GIs (GI numbers are being phased out by NCBI)
Map to reference / de novo assembly: Properties (i.e. values added in the Info viewer) of the reads are now copied to all contigs produced (previously these were only copied to small contigs)
Map to reference / de novo assembly: Fixed some consensus options (e.g. trim to reference sequence, call N if low coverage) not being applied when the reads being assembled have no quality
Map to reference / de novo assembly: On machines with at least 16 processors, assembly uses one processor fewer in order to leave a processor for garbage collection to prevent runaway memory usage on powerful machines. This can be configured with the advanced preference called MaximumThreads.ReduceByWhenAtLeast16Processors
DESeq2 Compare Expression Levels: Fixed incorrect handling of replicates, added support for multiple chromosomes, improved documentation, improved performance, fixed coloring of results
BBTools: Upgraded to version 36.92
Translation: Extracting a translation to a new document from a CDS annotation now respects the NCBI annotated translation property (which should include the effects of NCBI transl_except properties)
Transfer Annotations: Added option to not merge annotations of the same type and region into a single annotation
Transfer Annotations: Prevented transfer of annotations that are completely or partly outside of the reference sequence and can't be truncated
Annotate from database: Now works with BLAST results in the source database
Find Variants/SNPs: On circular contigs without a reference sequence, removed incorrect additional variants found past the wrap around position
Workflows: Added advanced option in workflow steps called 'If this workflow step fails, silently continue using only successful data sets'
Workflows: Added 'Extract Reads from Contig/Alignment to List' to operations which can be added as a workflow step
Workflows: Improved 'Group Sequences into List' step to produce more efficient lists when grouping stand-alone sequences
Workflows: Fixed bug where they would produce inconsistent results on operations that used enzyme set options (because they would use the most recently selected enzyme set from a non-workflows operation)
General: Fix bug where many operations would unnecessarily load the entire document before showing options
General: Fix bug where right clicking in folder tree doesn't select the clicked-on folder
General: Fix bug where 'between base annotations' of genbank files are not handled correctly
General: Added advanced option in Preferences to set user name to be used when recording document history
General: Fixed crash on systems that don't support custom cursors
Sequence View: Now records the user name of the person responsible when an annotation is created or edited (uses the same name as document history)
Sequence View: Text inside annotations in the circular view is positioned a bit further away from the edge of the annotation if possible
Sequence View: Fixed crash in rare situation when deleting primers
Sequence View: Fixed crash editing in the circular overview while an operation is running on that sequence
Sequence View: Fixed crash when saving a sequence with large tracks while an operation is running on that sequence
Set Paired Reads: Added option (default on) to delete the unpaired source documents when pairing by pairs of sequence lists
BLAST: Updated Geneious default values to reflect default values on NCBI BLAST website
NCBI BLAST: Display more information about some NCBI Server failures
Custom BLAST: Fix bug where creating a BLAST database from BLAST hits causes full download to fetch from original BLAST database
Custom BLAST: Update executable files for 32-bit platforms to their respective latest valid release
Cloning: Ligate and Concatenate sequences with compatible overhangs no longer discard annotations located within reverse-directed overhangs
Lineage: Information about extracted annotations and regions are now updated for active links when parent sequence gets modified
Online Resources: Quickstart Guide link has been replaced with a link to our Quickstart video
GenBank Files: Fix crash when parsing Comments section where automated annotations don't have an end-tag
Document Table: No longer displays columns if none of the documents have a value for that column
Convert to Oligo: When reconverting an existing oligo, will now respect the binding region rather that recalculating for the entire oligo
Convert to Oligo: Will now always replace any standalone sequences in the selection. Previously, would only replace them if every document in the selection was a standalone sequence
Geneious Server: Fixed crash in some situations when downloading results from Geneious Server to a different computer than that which ran the operation

New in Geneious Prime 10.0.9 (Jan 25, 2017)

New in Geneious Prime 10.0.8 (Jan 18, 2017)

New in Geneious Prime 10.0.7 (Dec 14, 2016)

New in Geneious Prime 10.0.6 (Nov 23, 2016)

New in Geneious Prime 10.0.5 (Oct 27, 2016)

New in Geneious Prime 10.0.4 (Oct 25, 2016)

New in Geneious Prime 10.0.3 (Oct 18, 2016)

Bugs Fixes and Minor Changes:
Annotation Table: Table can now be exported in tab separated values (TSV) format
Annotation Table: Fixed commas not being stripped from numbers before export
Map to reference / de novo assembly: Fixed crash in some situations when data contains non-N nucleotide ambiguities
Cloning: Fixed broken lineage for cloning operations after importing documents
Cloning: One-Line warning in cloning options is more informative
Restriction Cloning: Fixed broken lineage when re-running an operation after changing the underlying sequence
Restriction Cloning: Fixed bug where the terminal ends on circular products weren't updated correctly
Restriction Cloning: Fixed failing digestions if the product is linear and a terminal reaction is on a circular sequence
Restriction Cloning: Fixed warning that indicated that an additional cut site was outside chosen cut sites but which was actually internal on inserts that span the origin of a circular pre-digested fragment
Golden Gate: Fixed crash when running the operation using pre-digested sequences
Golden Gate: Fixed crash when running an operation that requires PCR on a sequence that uses exactly one primer with an existing overhang extension
Find Restriction Sites: Fixed bug where in some cases restriction sites were not found
Updated NCBI BLAST databases
NCBI: Fixed problem accessing https sites such as NCBI when via a web proxy
Tree builders: Fixed NPE when cancelling a tree inference with the 'Mask Alignment' option checked
Tree builders: Fixed NPE when building tree on sequence lists imported from fasta format
Mask Alignment: Fixed bug where progress could appear to go backwards if stripping a mask in a track with a very large number of intervals
Workflows: Fixed crash (or text being drawn in wrong location) when viewing a workflow that contains a workflow which contains custom Java code you didn't write yourself
Workflows: Fixed crash when attempting to use copy/paste shortcut keys on steps in a workflow, this is now disabled
Sequence/Contig View: Fixed crash when using annotation filter while a trim annotation is selected
Transfer annotations: Fixed crash when running on multiple documents
VCF Export: Fixed genotype being ignored when exporting
Plugin Development: Fixed crash moving documents to a hidden folder in a shared database

New in Geneious Prime 10.0.2 (Oct 4, 2016)

New in Geneious Prime 10.0.1 (Oct 4, 2016)

Bugs Fixes and Minor Changes:
Restriction Cloning: Various usability improvements and bug fixes
Workflows: Added 'Randomly Sample Sequences' workflow for randomly sampling (without replacement) a specified number of sequences from a list
Workflows: Added 'Copy Document(s)' bundled workflow which can be used as part of variant finding workflows to prevent annotating of the input reference sequence
Workflows: Extract Sequences by Name: Added option to extract each set of sequences that match a specified partial name to a separate document
Workflows: Fixed crash when using copy/paste on steps in a workflow
Workflows: Fixed being unable to run workflows with assembly steps with custom trim options
Workflows: Workflows hidden from the drop down menu are now able to be included as steps in other workflows
Workflows: Fixed bug preventing running of workflows with an export step with an exposed option for the folder to export to
Workflows: Fixed crash trying to set export options for SAM/BAM format
Workflows: Fixed crash after running a workflow step that actively links documents and later modifying one of the input documents. Workflows now no longer attempt to actively link documents
3D Structure viewer: Fixed a crash that would happen on some documents
Tree Viewer: Made support values near the root end up in correct positions after re-rooting a tree
Sequence/Alignment View: Right click within a sequence no longer automatically selects the entire sequence when nothing is selected. Added a popup menu option to select the entire sequence
Sequence/Alignment View: Right click menu 'Add Annotation' is now enabled when nothing is selected to allow creation of annotations between positions
Sequence/Alignment View: Fixed mouse cursor getting stuck on a busy cursor sometimes when saving
Sequence/Alignment View: Turning off the checkbox to show any annotations no longer turns off the annotate and predict checkboxes (e.g. Find ORFs or Find Restriction Sites)
Sequence/Alignment View: Fixed bug where pressing Enter in the annotation filter box prompted to edit the sequence name
Sequence View: Fixed crash when displaying 3-letter amino acid codes
Sequence View: Fixed zoom to selection not zooming in enough sometimes when wrapping is on
Sequence View: Alt-dragging over the origin of circular sequences now zooms to that region correctly
Alignment View: Fixed copy annotations in selected region to another sequence wrongly disabled
Alignment View: Fixed out of memory or poor performance copying annotations between reference sequence and consensus in a large contig
Contig View: Fixed poor performance when deleting regions of large contigs
Circular Overview: Fixed incorrect editing results after setting a sequence as circular and using undo
Circular Overview: Alt-left mouse drag now zooms to the selected region
Circular Overview: Fixed crash and/or wrong sequence showing on genome sequence lists
Circular Overview: Fixed inaccurate green box which indicates the currently displayed region
Transfer Annotations: Transferred annotations that extend beyond the aligned region of the annotated sequence and the reference will now be truncated (does not apply to circular alignments)
Annotate From Database: Annotations with multiple intervals that cross the origin can now be used to annotate similar regions on other sequences
Wrapper Plugins: Fixed crash when adding new files while renaming the plugin
Document Table: Fixed Paste Without Annotations for all Sequence Lists
16s Biodiversity: Added an upper limit of 500 characters for the job description, longer descriptions submitted from previous versions will be truncated
Mask Alignment: When creating a new alignment with sites removed, sequences are no longer renamed by default
Mask Alignment: Saving a new document with sites removed now works when multiple documents are selected
Map to reference: Fixed mapping reads to all locations sometimes not mapping gappy reads to all inverted repeat regions
Map to reference: Fixed discovery of incorrect structural variant insertions around repeat regions
Map to reference: Fixed so that structural variant junction IDs don't skip some values (i.e. they are now numbered consecutively starting from 1)
Map to reference: Structural variant deletions are now represented as reads with gaps rather than split reads for deletions up to the maximum of 1000 bp or the maximum read length, whichever is larger
Map to reference and de novo assembly: Made it faster
Trim Ends: Fixed progress not moving and cancel not working when running slow trimming operations (e.g. primer trimming)
De novo assembly / Map to reference: Fixed rare crash in some situations
BBTools: Upgraded to version 36.32
CloneManager CM5 Importer: CloneManager-specific annotation types have been replaced with standard Geneious annotation types
Lineage Viewer: Fix end index being off by two when linking a reverse direction child to its extraction parent
Ligation: Fixed bug where sequence lists couldn't be ligated
Similarity Search: Fixed crash when there is an alias in a folder being searched
Paste with Active Link: Fixed so that it works correctly in conjunction with 'Copy (reverse complement)'
Extract with Active Link: Fixed bug where an extraction was not actively linked if the extraction started and finished at the ends of the source sequence
Parent/Descendant Viewer: Now correctly updates linked intervals when a parent document change is propagated to a child
Chimera Filtering: A notification that the USEARCH version is not supported will now be displayed if Remove Chimeric Reads is run with USEARCH v9
Chimera Filtering: Added SILVA to the list of reference databases
Chimera Filtering: Made UCHIME failure messages a bit more user friendly
Primer Design: Fixed crash when running Test with Saved Primers with reverse complementary forward and reverse primers
General: Fixed memory leak of up to 2 MB per operation run
General: Fixed crash when dealing with invalid imported protein sequences
Other Notes:
The Geneious Software License Agreement has been updated. You can access the most current version through Geneious by going to Help -> Online Resources -> License Agreement

New in Geneious Prime 10.0 (Oct 4, 2016)

FEATURES:
Clone Manager Import for molecule files (.cm5)
Text Document creation and editing - Create a blank text document via File > New and edit plain text documents inside Geneious
Variant Finding / SNP Trees: Added a workflow to apply discovered variants to the reference sequence in order to create a variant sequence. This is useful for the creation of SNP trees
New Sequence: Added the ability to specify a binding region to simplify entering primers or probes that have extensions
Cloning: Create active parent/descendant links when pasting a sequence using 'Paste with Active Link' in the right-click menu of the Sequence View
Aliases: Store a single document in multiple folders simultaneously using 'Paste Alias' in the Edit menu or by holding Ctrl+Shift when dragging (Cmd+Alt on macOS)
Folder Search: Find folders by name in the Sources Panel by typing a keyword and pressing Enter
Restriction Cloning:
Completely redesigned to be much simpler and more powerful
Automatic identification of compatible cut sites from any number of annotated or un-annotated enzymes
Manual controls for choice of cut site and treatment of sticky ends such as blunting and filling
Digest and ligate any number of sequences in one step with drag and drop ordering of fragments
Embedded sequence view shows target region for each fragment
Alignment Masking:
Mask alignment sites that should be excluded when tree building by adding a Masked annotation to the consensus instead of deleting the site completely
Choose whether or not to exclude masked sites when running any of the tree builders available for Geneious
Choose whether to gray-out or completely hide masked sites in the Alignment View
Automatically mask sites according to various criteria using 'Mask Alignment' in the Tools menu (previously called 'Strip Alignment Columns')
Store multiple alternative masking patterns on the same multiple alignment using annotation tracks
Import masks from the EXSETs defined in the ASSUMPTIONS block of NEXUS files
New option to mask or strip sites according to user-defined ranges of sites, or strings of 0's and 1's using 'Mask Alignment' in the Tools menu
Mask Alignment now ignores trimmed regions of sequences when determining if a site contains ambiguous states
Mask Alignment now ignores end gaps when computing the percentage of gaps (for contig alignments only)
Mask Alignment now ignores gaps when determining if a site contains all identical nucleotides/amino acids
Chimera Filtering:
Filter chimeric reads from sequencing data by comparing to a reference database using 'Remove Chimeric Reads' in the Sequence menu
Choose between the bundled public domain UCHIME algorithm or the faster USEARCH implementation (USEARCH must be downloaded separately)
Use any sequence list or alignment as the reference database, links and instructions for importing suggested databases are included
Parent/Descendant Improvements:
Lineage View is now easier to access as a separate tab
View the options used when an operation was run by clicking 'Show Options' in the Lineage View (for supported cloning operations only)
Even more information about operations is now shown in the Lineage View
The region of sequences used in an operation is now shown next to each sequence in the Lineage View
'Go to' in the Lineage View now selects the region of a sequence that was used
Assembly:
Structural Variant Mapping: Adding support for insertion discovery when the ends of a read map to nearby locations but the center of the read doesn't map
De Novo Assembly: Better results when assembling Ion Torrent, 454, and PacBio CCS data
Map to Reference: Better results when mapping Ion Torrent, 454, PacBio CCS and PacBio CLR data
Map to Reference and De Novo Assembly: Faster on long reads (e.g. PacBio)
Sequence/Alignment/Contig View:
Circular Overview: Added a setting to show a zoomed out overview of circular sequences
Total number of non-gap nucleotides or amino acids now shown in Statistics tab
Three letter amino acid codes can now be shown by zooming in to 200% on protein sequences or by turning on 'Three letter amino acids' in the translation controls for nucleotide sequences
Sequences that contain a selection or have the cursor in them are highlighted with a different background color
Go To Base now allows selection of region that crosses the origin for circular sequences
Shortcut key added for editing the selected sequence's name or other displayed field (default F2)
Scroll past the origin of circular sequences using scroll wheel, panning or left/right arrow keys
BUGS FIXES AND MINOR CHANGES:
Sequence/Alignment/Contig View: When showing numbering on all sequences, fixed so that reversed reads are always numbered in reverse
Sequence/Alignment/Contig View: Fixed small rendering glitches for single bp annotations in some situations
Sequence/Alignment/Contig View: Fixed poor performance / out of memory when deleting millions of sequences
Sequence/Alignment/Contig View: Add annotation no longer creates additional intervals for regions between nucleotides in some situations
Sequence/Alignment/Contig View: Fixed crash when trying to apply trimming results to an unselected document after starting another operation on it
Sequence/Alignment/Contig View: Fixed crash in some situations when undoing while live annotate & predict annotations are showing
Sequence/Alignment/Contig View: Fixed poor performance (and occasional crash) when running low on memory while loading a large annotation track
Sequence/Alignment/Contig View: Fixed rendering bug on Linux platforms where parts of reference sequence and consensus are drawn over the top of reads in rare situations
Sequence/Alignment/Contig View: Fixed hang or poor performance sometimes when alt/command dragging a region to zoom to
Sequence/Alignment/Contig View: Fixed when extracting regions containing duplicate annotations (e.g. FreeBayes variant calls with ploidy 2) to preserve duplicates rather than converting to a single annotation with duplicate intervals
Sequence/Alignment/Contig View: Fixed incorrect highlighting of differences in reads spanning the origin of circular contigs when hiding columns of gaps
Sequence/Alignment/Contig View: Fixed integer overflow when drawing annotations on very large circular contigs and sequences
Sequence/Alignment/Contig View: Fixed crash sometimes when saving after deleting sequences
Sequence/Alignment/Contig View: Added advanced setting to control the threshold for the number of sequences above which editing history annotations aren't created
Sequence/Alignment/Contig View: When extracting an unapplied 'Live Annotate & Predict' annotation, that annotation is now included in the extracted sequence. This also fixes a crash when extracting an unapplied primer annotation
Alignment/Contig View: Fixed poor performance viewing large contigs with coloring by annotation on or wrapping on
Alignment/Contig View: Fixed consensus name missing when wrapping is on
Alignment/Contig View: Improved performance when viewing large contigs and increased threshold to allow viewing more reads before it hides reads when zoomed out too far
Alignment/Contig View: Fixed unnecessary prompt about applying changes to referenced sequences after transferring annotations to the consensus sequence.
Alignment/Contig View: Fixed crash after extracting sequences when the same alignment has unsaved changes in another window
Alignment/Contig View: Removed incorrect warning about editing when pressing a shortcut key containing ctrl and shift on MacOS
Alignment/Contig View: Fixed crash sometimes when running tools which annotate sequences
Alignment/Contig View: Fixed consensus annotations discarded when extracting an alignment from an alignment
Alignment/Contig View: Fixed the names of tracks with long names being rendered over the top of annotations on alignments that also contain a tree
Sequence View: Fixed number of bp selected message appearing in wrong location sometimes while dragging on a circular sequence
Sequence View: Fixed 'Go to base' crash when choosing to select a different sequence from a genome sequence list
Sequence View: Fixed crash when switching between large annotated linear and circular sequences in the sequence selector
Alignment/Tree View: Fixed edit of field in Alignment View not propagating to corresponding tip label in Tree View
FASTQ and FASTA paired read exporters: Improved performance and also now works on contigs
Coverage Graph: Fixed to not draw log scale label when there isn't enough space for it
Sequence Logo Graph: Fixed crash on large contigs after flagging the reference sequence as not a reference sequence
Wrapper Plugins: Fixed crash when running a newly created wrapper plugin on a non-matching set of selected documents
Tree Building: Fixed crash if you delete sequences from a list so that there are under three sequences, then run tree building and save changes when prompted
Tree Building: Changed Jukes-Cantor equation used to calculate protein sequence distance matrix to be more accurate
Translation: Fixed poor performance working with translations of millions of sequences
Annotations Table: Fixed Geneious becoming unresponsive while exporting a large table to CSV
Document Table: Fixed Paste Reverse Complement and Paste Without Annotations for multiple documents, Sequence Lists, and Alignments
Map to reference: Fixed crash when a paired read in an existing contig was flagged as the reference sequence
Map to reference: Fixed map to all locations sometimes excluding locations on the other strand when the alignment could contain different but equally valid positions for gaps
Map to reference: Fixed excessive memory usage when mapping large contigs to a reference sequence
Map to reference: Fixed excessive memory usage and poor performance when iteratively mapping to a very large reference sequence
Map to reference: Fixed mapping reads to all locations sometimes not mapping gappy reads to all inverted repeat regions
Mask Alignment: Sequences containing only gaps are excluded from the result when stripping sites
Mask Alignment: Fixed wrongly removing annotations present on the consensus sequence
Assembly Options: If trim options inside assembly options have been modified from default values, the trim "Options" button now indicates that by changing its label
BBTools: Upgraded to version 36.11
Trim using BBDuk: Added link to actual sequences used for bundled adapter lists
Trim using BBDuk: Turned on 'Keep original order' setting by default to ensure that rerunning it produces the same results each time
Error Correct and Normalize Reads: Exposed number of threads setting since results vary depending on the value of this setting
BLAST: Fixed crash if you delete the the folder containing the results while BLAST is running
BLAST: Fixed BLAST giving incorrect results when running a Discontiguous Megablast due to parameters being incorrect
BLAST: Fixed a problem where NCBI BLAST always used the default match scoring values regardless of what was chosen
BLAST: Fixed BLAST not importing all result from search or file
BLAST: Updated BLAST+ executables to v2.4.0
Custom BLAST: Fix a problem where downloading/setup process of custom BLAST does not recover from network failure
Custom BLAST: When a large batch blast is cancelled we now immediately stop all iterations of that job
Document History: When viewing options that have other options accessible via a button (e.g. the trim options inside assembly options), the button is now enabled so that you can view the other options
Workflows: If documents created would have the same name as an existing document in the same folder, the name has a number appended to make it unique (like all non-workflow operations already behaved)
Workflows: Fixed out of memory error when running workflows which produce multiple documents
Workflows: Fixed sequences not being extracted using Extract Sequences By Name when the names to extract are on new lines
Workflows: Fixed crash sometimes when selecting a custom icon
Workflows: Now available from the toolbar by default
Set Paired Reads: Fixed icon incorrectly showing inwards pairs when used on existing paired reads with different orientations
General: Fixed crash in some situations when out of disk space
General: Fixed crash when deleting a folder at the same time as a sub-folder
General: Added warning before pasting more than 1 million characters in to various text fields (may cause hang)
General: Proxy settings should update now when proxy.pac changes
General: Fixed opening links to files in Finder (Mac OS X)
General: Fixed crash sometimes when attempting to change your data location to a read only folder
General: Expand/collapse buttons no longer disabled when showing read-only options (eg. from History and Operations table)
General: Added parent/descendant information to documents produced by Annotation Generators (Mask Alignment and Codon Optimization tools)
General: Icon or text shown next to cursor when moving documents and folders by drag and drop
General: Confirmation about erasing all deleted items on startup no longer disappears
General: Importing folders now asks before re-using an existing folder and defaults to creating a new one
General: Tips are now shown while Geneious is loading instead of when there isn't a document selected
General: Further improvements of fonts in Tutorial/help panel and in other components for HiDPI displays
Text View: When viewing nucleotide quality scores over 99, these are now clipped at 99 in order to make the text view readable
Shared Database: Fixed a crash that would occur when running a BLAST search from a read-only folder
Clean Install: Fixed an incorrect message about 'Geneious Education plugin not installed' sometimes after changing your data location to a different drive from the Welcome to Geneious dialog.
Fasta Import: Fixed crash sometimes when importing amino acid and nucleotide fasta files together
FastQ Import: Fixed out-of-memory error produced when importing corrupted GZip FastQ files
GFF Import: Fixed document size after importing wrongly appearing as much smaller than it really is
GFF Import: When import fails due to invalid characters, the importer will now mention what those chracters are
GFF Export: Fixed frame/phase being lost when exporting
SAM/BAM Export: Added option whether to export reads in alignments that don't map to the reference sequence
SAM/BAM Import: Show warning message when input reads are outside the reference sequence
Genbank Import: Fixed error that would occur importing documents with "bp", "aa" or "rc" in their names
Codon Optimization: Fixed crash with some sequences that should be rejected for having ambiguous bases or gaps
Primer Design: Updated Primer3 to version 2.3.7 see the release notes for more information.
Tutorials: no longer display wrong images when two tutorials use the same image file names
DNAStar Import: Fixed a bug that caused import to fail on files containing an empty line between the feature table and sequence
NEXUS Import: Fixed null pointer exception when parsing files with a DATA block when taxa in trees and alignment don't match
PIR/NBRF Import: Fixed crash when attempting to identify a nearly empty FASTA file
Vector NTI: Fixed a crash when importing amino acid sequences with parent/child relationships
Lineage View: Fixed bug where parent lineage information from some operations was lost after restarting Geneious
Keyboard Shortcuts: No longer allows setting ALT key shortcuts that don't work because they are assigned to menu items
Wrapper Plugins: Fixed crash when selecting a folder rather than a file as the wrapper plugin executable
Biocode Plugin: Fixed crash when pressing the shortcut key to edit a property of a document in the document table when nothing is selected
Annotate from database: Added option to disable merging of matches with the same type and region
Agents: No longer available from the toolbar by default or from search options, but are still available under the View menu. Can be added back to the toolbar via right-click on the toolbar
Tutorials: Now support https links
Tutorials: Built-in tutorial has been completely rewritten
OTHER NOTES:
Geneious now requires Java 8 and will no longer run on earlier versions of Java (including legacy Java for Mac OS). This means Geneious will no longer run on platforms where Java 8 is unsupported such as Mac OS X 10.6 (Snow Leopard) and 10.7 (Lion)

New in Geneious Prime 9.1.6 (Sep 20, 2016)

New in Geneious Prime 9.1.5 (Jun 13, 2016)

New in Geneious Prime 9.1.4 (May 10, 2016)

New in Geneious Prime 9.1.3 (Apr 5, 2016)

Bugs Fixes and Minor Changes:
BLAST: Prevent results from different searches being delivered to the same folder for UniProt/Swiss-Prot
BLAST: Prevent results folder from being deleted when a search is canceled if the folder already contains data
BLAST: Fixed a problem that caused BLAST hits to be exported in a format incompatible with previous versions of Geneious
Consensus Tree Builder: Fixed crash that could happen on trees with no branch lengths
Sequence/Contig/Alignment Viewer: Minor improvements to make nucleotides/amino acids appear less blurry
Sequence/Contig/Alignment Viewer: Fixed so that trim annotations are the same thickness as they were before 9.1
Sequence/Contig/Alignment Viewer: Trim annotations are now hidden by default in all views except on a single sequence or pairwise contig
Sequence/Contig/Alignment Viewer: Fixed hang sometimes when selecting a region in the consensus on very high coverage contigs
Sequence/Contig/Alignment Viewer: After editing an annotation, fixed rare situation where clicking may crash or not select the next annotation clicked on
Contig/Alignment Viewer: Fixed potential loss of saved changes when applying changes to referenced sequences while running low on free memory
Contig Viewer: Fixed rare crash when viewing some contigs at a zoom level close to the point where it hides reads when zoomed out too far
Contig Viewer: Fixed crash if you set a paired read as the reference sequence and choose link paired reads in the layout options
Sequence Viewer: Fixed crash when viewing circular chromatograms
Sequence Viewer: Fixed excessive reloading of viewer and potentially lots of 'too many tracks' dialog messages when calculating expression levels
Circular Contigs: Fixed so that reverse complementing a circular contig gives correct results now
Circular Contigs: When editing a circular contig with a reference sequence to insert ot remove gaps from the reference sequence, the circular contig length now updates correctly
Circular Contigs: If you change the reference sequence and extract that sequence, the extracted sequence is no longer incorrectly marked as circular
Sequencing Preferences: Increased the maximum allowable values for medium and high quality base coloring thresholds from 99 to 30,000
Save as EPS/EMF format: Fixed crash or bad looking images when 'Shaded annotations' option is on by disabling the option for EPS and EMF formats
Map to reference: Fixed bug where it would unnecessarily introduce gaps sometimes
Map to reference: Fixed crash sometimes when the option to find structural variants is on
Map to reference: Fixed incorrect mapping quality in some cases
De Novo Assembly: Fixed wrongly showing warning sometimes about too many contigs when assembling fewer than 100 sequences
Find Repeats: Fixed crash sometimes when allowing a high percentage of mismatches
Start up: Fixed crash on startup on some Windows systems when trying to access a data location on an unreliable network drive
Start up: Improved start up behaviour when previous data location is not there. It now always prompts to choose a data location in this situation and won't allow you to pick an invalid location
General: Fix some text areas not being adjusted for larger font sizes and HiDPI displays
EndNote import: Prevent it from attempting to import unrecognized xml files
Trim by Vector: Fixed a problem where operation would continue in the background when cancelled
Geneious Server: Fixed bug where if the input documents to an operation were in different folders, the input documents would be copied into the destination folder
Save As will no longer move documents between folders if the original folder is not selected
Contact Support: Fixed problem where pressing enter in the message field could send the message unexpectedly
Cloning from Workflows: Fixed crash when running a restriction cloning from workflow with inserts with two annotated cut sites
Fasta Import: Fixed a problem where auto-detect did recognise FASTA file if whitespace appeared in the first sequence
CSV/TSV Import: Fixed the preview becoming too wide for the import options window
Gibson Cloning: Fixed bug where it could not propagate changes on imported documents that involved a Gibson Operation
Gibson Cloning: Uses origin of the backbone if it's an extraction that contains the origin
Tree viewer: Fixed crash that could happen when filtering nodes in a tree while applying actions to that tree
Shared Database: Minor improvements to prevent duplicate search index in shared database
Extract PCR Product: Now keeps all primer bind annotations in the product, instead of discarding those not used for the extraction
NCBI Search: Fixed so that when NCBI has internal server errors they are reported instead of returning no results from the search
Fixed a bug where new installations of Geneious wouldn't remember existing proxy server preferences
Trees: Fixed a crash that would occur when swapping taxon names in some tree documents

New in Geneious Prime 9.1.2 (Feb 29, 2016)

New in Geneious Prime 9.1.1 (Feb 29, 2016)

Bugs Fixes and Minor Changes:
Data Location: Warns that if you set your Geneious data location to a Google Drive, OneDrive, iCloud Drive, or DropBox folder, it could cause data loss or crash Geneious if these don't completely synchronize before you use Geneious from another location
Keyboard shortcuts: If you try to assign a new shortcut already assigned to something else it now removes the shortcut from the other action after warning about it
Fasta Import: Fixed failure while importing UTF-8 BOM encoded fasta file
Mean Coverage: Fixed mean coverage in document table incorrectly handling trimmed regions in some cases
Sequence Viewer: Fixed width of sequence track "Options" button on Mac OS X
Sequence Viewer: Increased default annotation thickness in circular views
Sequence Viewer: Fixed annotations coming back after restart if all are deleted from NCBI gene documents
Sequence/Contig/Alignment Viewer: Fixed occasional crash
Sequence/Contig/Alignment Viewer: Fixed text inside annotations extending outside the ends of the arrows sometimes
Sequence/Contig/Alignment Viewer: Fixed images next to names, graph scale bars and graph heights for HiDPI displays
Sequence/Contig/Alignment Viewer: Fixed crash in rare situations on MacOS after ctrl-clicking
Contig Viewer: Fixed annotations spanning the origin of the reference sequence in a circular contig not being rendered near the start of the sequence
Contig Viewer: Fixed clicking RNA seq / structural variant link sometimes appearing as fewer than three fading gaps even when there are at least 3 trimmed nucleotides
Contig Viewer: Fixed deleted trim annotations sometimes reappearing after saving
Contig Viewer: Fixed bug where trying to create undirected annotations on circular contigs would create directed annotations instead
Map to reference: Fixed paired read handling when spanning large deletions or introns where it would sometimes incorrectly trim the entire read due to wrongly thinking paired reads overlap
Map to reference: Fixed crash sometimes when finding structural variants when mapping to a circular reference sequence
Map to reference: Fixed structural variant mapping annotations not appearing sometimes
BBTools: Upgraded to version 35.82
Ace Import: Improved the message displayed when the imported file has certain errors
SAM/BAM Import: Fixed poor performance and excessive memory use when importing RNA seq data with large introns or DNA data with large deletions. Large introns/deletions are now annotated during import with reads spanning them split into 2 parts with hyperlinks between them
GFF Import: Fixed crash when importing files that don't quite adhere to the GFF format (e.g. GFF files exported from earlier versions of Geneious)
Import: Fix poor performance or out of memory crash when importing a pair of large files
Find CRISPR Sites: Fixed crash that could happen when running CRISPR on sequences with unsaved changes
Improved Splash-screen and other icons for HiDPI displays
Nexus/Newick Exporter: Branch length will be exported as Standard Numeric format now rather than in a Scientific notation
Save as Image: Fixed crash that could happen when exporting very large images as JPEG
Primers: Fixed crash that could happen when designing for a region entirely beyond the end of a sequence
Licensing: Geneious will now correctly check the expiry date of subscription licenses when checking for new versions
Licensing: Fixed incorrect warning displayed for certain subscription licenses saying they are not valid for current version
Spreadsheet Importer: Can now import .TSV files of the kind that Google Sheets exports
Spreadsheet Importer: fixed a couple of bugs relating to documents of various charsets not importing high unicode characters properly
Always extract primer sequence for mismatching primers while extracting PCR product for list of sequences or multiple sequences

New in Geneious Prime 9.1 (Feb 29, 2016)

Features:
Alignment Viewer: Uses colors from tree viewer as the background color for each sequence
Alignment/Contig Viewer: Added option to ignore ambiguous disagreements when highlighting or using 'go to next disagreement'
Alignment/Contig Viewer: Added option to skip to the next column when using 'go to next disagreement'
Alignment/Contig Viewer: Made it possible to go to next or previous disagreement in current sequence or reference sequence only without using shortcut keys
Text Importer/Exporter: Geneious can now import, store, display, and export plain text and html files
NCBI: Added hyperlink to Pubmed articles
Gibson Assembly: Added ability to chose exonuclease activity to enable operations such as SLIC, SLiCE, CPEC, InFusion and GeneArt Seamless Cloning
Map to reference: Added workflow to map multiple sets of reads to their corresponding reference sequence with the same name or name prefix
Lineage View: More information about operations is now shown in the parent and descendant trees
Lineage View: New "Save as HTML" button to save parents and descendants as bullet points for reporting
CRISPR Site finder: Now accepts sequence lists and groups of sequence documents, allowing for batch discovery and scoring of CRISPR sites
UniProt: Updated search fields to better match the options available on the website
General: Added ability in Operations table to display the options used for a running operation
General: From operation options dialogs, can set keyboard shortcut and/or add button to toolbar to run the operation in future
General: Operations without icons are now able to be added to the toolbar by right clicking on it or from a button in preferences
General: Further improvements for larger font sizes and HiDPI displays
Bugs Fixes and Minor Changes:
Annotate from database: Restore defaults button no longer restores the folder to its default value. The folder can be restored to its default value independently from the folder chooser
CSV/TSV importer: When importing to a list, the document name created now matches the imported file name
CSV/TSV importer: Can now import huge files using very little memory
Map to reference: Fixed crash choosing an empty folder as reference sequence
Map to Reference: Fixed crash when input reads are modified while mapping is in progress
Map to Reference: Fixed crash selected a folder containing a mixture of lists and stand-alone sequences as reference sequences
Startup: Fixed crash on startup when Geneious does't have permission to write to your Geneious data location
Startup: Fixed crash during FLEXnet installation on some windows systems
Find In Document: Now ignores leading and trailing spaces on the text to find
Sorting documents: Fixed rare crash when sorting by a column that contains a mixture of numbers and non-numbers
Sequence Viewer: Improved sorting of sequences within a sequence list so that names with numeric values are sorted numerically
Sequence Viewer: Fixed hang on very large sequences when viewer panel is resized down to less than 4 pixels wide
Sequence Viewer: Uses OpenSans font bundled with Geneious on all platforms. By using a known font, text can now be better positioned so it looks much nicer
Sequence Viewer: Improved rendering of text in circular views so that it is more readable and also text is no longer drawn upside down in the lower half of the view
Sequence Viewer: Fixed rare crash when editing primer annotations
Sequence Viewer: Fixed double clicking to edit an annotation not working if you click near the right-hand side of the annotation
Sequence Viewer: Fixed crash changing annotation generator settings while generated annotations from another tool are selected
Sequence Viewer: Fixed problem where mouse cursor could disappear when running BLAST while viewing a circular sequence
Sequence Viewer: Fixed crash sometimes when printing or saving to an image after turning off all annotations
Sequence Viewer: Fixed crash sometimes when selecting a region outside the bounds of a circular sequence when it is in a list containing longer sequences
Sequence Viewer: Fixed crash attempting to 'apply selected annotations' when the same document has unsaved changes in a different window
Sequence Viewer: Change Residue Numbering on linear sequences now skips zero when including negative numbers
Alignment Viewer: Stopped it adding (modified) to alignment name when just editing annotations
Contig Viewer: Fixed crash in rare situations when editing a contig
Contig Viewer: Fixed reads not showing up sometimes when printing or saving to image
Find Variants/SNPs: No longer filters variants due to strand-bias near of the sequenced region for paired reads. Previously this logic only applied near the ends of the reference sequence rather than the sequenced region.
Find Variants/SNPs: Fixed crash or wrong results if the reference sequence is not the first sequence in an alignment or contig
Save image as PDF: Fixed so that shaded annotations look correct
RaxML: Consensus support values are now shown by default and can be displayed on branches
RaxML, FastTree, Garli, BBTools: Documents produced now have the same description as input documents
Document Table: don't automatically add "modified" to names of documents
Golden Gate: Complementary primers get created at nearest cut site instead of at the sequence end
Golden Gate: Creates 20bp primers by default if using primer extension and warns user if the sequence is shorter than 40bp when not using existing primers
Golden Gate: Fixed crash showing options from history of imported assemblies
Golden Gate: Fixed crash showing options from history when some of the documents with primers have been deleted
Golden Gate: Fixed incorrect overhang handling for pre-existing overhangs
Golden Gate: Fixed enzyme cut sites being introduced when creating random overhangs
Golden Gate: Show warning if pre-existing overhangs are different to the overhang created by the selected enzyme
Golden Gate: Warning correctly shows the actual overhang instead of always the overhang on the top strand
Toolbar: Fixed bug where items would sometimes go missing from the toolbar after customizing the items to display
Enzymes: Avoids crash on startup if a previous download of the enzyme set was not successful
SAM/BAM Export: Improved performance
Local BLAST: Include BitScore value in the result document fields
BLAST: Fixed crash or wrong sequences being searched when there are unsaved changes and it prompts to save when you click BLAST
BLAST: Changed NUM_ALIGNMENTS to 1000 (as response to this post) instead of to the value given in Maximum Hits
NCBI: Fixed DBSOURCE and DBLINK fields not being added to GenBank documents
NCBI: Fixed an infrequent bug where certain old GenBank documents had annotations that would cause the indexer to crash
Gibson Assembly: Fixed crash when performing the operation on some documents
VCF Exporter: Fixed allowing any IUPAC ambiguous bases instead of just N
VCF Exporter: Fixed crash when cancelling export during sequence track loading step
Workflows: Show warning if options have changed that make the workflow invalid
Tree Viewer: Fixed hang that could occur when viewing large trees with their branches ordered. Improved overall performance on these trees
Tree Viewer: Fixed crash that could happen when indexing a database with a tree document with a small, negative branch length
Shared Database: Fixed a problem that would cause the database to deadlock and cancel operation when multiple users add and edit documents in the same folder at the same time
Document Viewers: No longer allow documents to be modified in document viewers if they have an operation running on them
GFF Import: Fix wrong value in error message when lengths don't match and add sequence names to the error message when they also mismatch
GFF Export: Fixed when Export to strict GFF, certain character get escaped when it shouldn't according to GFF format standard
Primer Testing: Fixed an issue where a large amount of memory was being unecessarily used when generating mismatch annotations. Testing with mismatches should now use a lot less memory
Phylip Import: Fixed crash when importing file when some sequences appear to be probably nucleotide and others appear to be probably amino acid. The sequence type is now guessed by consider all sequences together
Lineage view: added additional information to 'Extraction' and 'Digest into Fragments' operations
Spreadsheet Importer: Now accepts carriage return-only line endings, which Google Sheets outputs
Batch Rename: No longer displays preview when being run from a workflow. In many cases the preview would not contain the correct values
GFF Import: Fixed the issue by putting the correct error/warning message to recognise empty GFF file and a GFF file without annotations
BED and GFF Importer:update the error message on importing the attached GFF file (with the FASTA) which contains duplicate sequences
Linux: Fixed crash on startup on Linux systems that don't support custom cursors
Feature Finder: Fixed a crash that occurs if searching large contig assemblies for a subset of features in a folder
Extract PCR product: Fixed a bug where Parent Descendant propagation would fail on sequences lists with only one sequence
De novo assembly: Fixed case where 'minimum overlap' setting was not respected
General: Fixed a crash that occurs when deleting multiple folders with the same name
Vector NTI: Fixed a failure to link parents and descendants when importing Vector NTI Advance archives with custom enzymes

New in Geneious Prime 9.0.5 (Dec 14, 2015)

Bugs Fixes and Minor Changes:
Improved dialog layout when clicking "More Options" or "Show Details"
CRISPR site finder: Fixed crash that could happen when scoring against an off-target database that includes protein documents
CRISPR site finder: Fixed crash that could happen when using a circular sequence with a selection starting at the origin
Keyboard Shortcuts: Run on incorrect documents after editing workflows or changing data location
Workflows: Can now configure trim step to remove existing trim annotations
Tree Viewer: Will not clip collapsed node labels off the edge of the default tree view anymore
Tree Viewer: Will not lay out space for labels when there are too many labels to display
Tree Viewer: Collapsed node labels will be colored by the color of the node, or black by default, and line up properly with branches
Tree Viewer: Collapsed node labels will use the same names as Tip labels, instead of the default taxon name
Tree Viewer: Disabled Species Delimitation plugin on large trees by default. This can be turned back on using advanced options
Contig Viewer: Fixed clicking RNA seq / structural variant link sometimes not jumping to the destination position in circular contigs
De novo assembly: Fixed crash or slightly wrong results in rare situations
Assemble by name or by sequence list: Contig names now respect the assembly name setting unless saved in a sub-folder
Shared Database: Fixed a deadlock that could occur if documents are added to a folder at the same time as documents inside the folder are being saved
General: Fixed hang sometimes when doing a full backup of your Geneious data
General: Fixed crash when running an operation from a secondary window when there is no sequence/alignment view
GTF Importer: Fixed bug where multi-interval annotations on the reverse strand were imported with intervals in the incorrect order
Cloning: Fixed crash on overhangs with more than one interval
Variant Finder: Fixed crash sometimes analyzing effects on translation when there are multiple variants within a single codon
SAM/BAM export: Fixed crash when exporting over approximately 700 million sequences to a single SAM/BAM file
NCBI: Download of WGS sequences now downloads all sequences mentioned in WGS & WGS_SCAFLD into a sequence list

New in Geneious Prime 9.0.4 (Nov 24, 2015)

New in Geneious Prime 9.0.3 (Nov 24, 2015)

Bugs Fixes and Minor Changes:
Local Documents: Fixed bug where if you view the contents of a folder while hundreds of documents are being added to it, some of those documents might not appear until you restart Geneious
Annotate from database: Include/Exclude types now matches on prefixes rather than the full annotation type text. This setting also applies to gateway annotations now
Annotate from database: Multi-interval undirected annotations are now supported as long as the intervals are ordered in the forward direction
Tadpole: Fixed crash when attempting to run tadpole on data which contains a read which is 0 bp long
Plugins: Plugins installed without administrator preferences are now installed to a location outside of your Geneious data location
Windows: Fixed some plugins failing to work after changing data location
Windows: Fixed crash changing Windows display settings while viewing operations table
Linux: Fixed flickering that would occur when performing some actions
Empty values in Meta-Data and New Sequence now show placeholder text on Mac OS
Workflows: Fixed bug introduced in 9.0.1 where only the first workflow change made after starting Geneious is saved.
Workflows: De novo assembly in a workflow can now configure the maximum number of contigs to generate and can configure it to use a subset of the full data set
Sequence Logo: Fixed crash on alignments with over 100,000 columns
Sequence/Alignment/Contig Viewer: Improved performance when saving to PDF/SVG
Alignment/Contig Viewer: Fixed incorrect translation of consensus sequence after editing but before saving
Alignment/Contig Viewer: Fixed incorrect translation frame when translating in frame of the consensus or reference sequence when it does not begin at the start of the alignment or around regions with gaps in both sequences
Alignment/Contig Viewer: Fixed shadow under viewers top panel on long sequences
Contig Viewer: Fixed incorrect rendering of trim sequences in circular contigs
Contig Viewer: Fixed clicking RNA seq / structural variant link sometimes not jumping to the destination position in the contig
Contig Viewer: Fixed clicking RNA seq / structural variant link sometimes not appearing as three fading gaps
Map to reference: When mapping an alignment to a reference sequence, sequence descriptions and properties are now preserved in the generated contig
Structural Variant Mapping: Fixed crash in some situations
Structural Variant Mapping: Added 'Rearrangement Distance'/'Fusion Distance' properties to annotations
Structural Variant Mapping: Improved detection of structural variants when there are nearby SNPs
De Novo Assembly: 'Assemble each list separately' setting can now be used in conjunction with 'Use X% of data' setting
Find Variants/SNPs: Fixed incorrect p-value calculation on merged variants in regions of high coverage
Fixed situation where some Linux distributions are unable to open clickable URLs within Geneious
Genbank Flat Importer: Now imports files correctly when qualifier values contain / characters
OneDrive: Fixed crash when you have partially synchronized your data with OneDrive and OneDrive has created conflicting files in your Geneious database. Using OneDrive (or any other file synchronization software) like this can lead to data loss so we strongly advise against using it
Dialogs: Improved buttons and icons for HiDPI displays
CRISPR Site Finder: Fixed problem where input RNA sequences would be scored as DNA when off-target scoring
CRISPR Site Finder: Fixed issue where CRISPR couldn't be run on some sequence lists, saying the target sequence was too short
CRISPR Site Finder: Fixed crash that could happen when an off-target database contained alignment documents or trees
CRISPR Site Finder: Will now run to completion on sequence lists when one sequence has no CRISPR sites, instead of cancelling early
Tree View: Fixed a problem where the Automatically Collapse Subtrees slider displayed the previous value rather than the current value
Tree View: Fixed a problem where the Automatically Collapse Subtrees slider would ignore changes on small trees
Tree View: Prevent the viewer hanging when viewing large trees with the Species Delimitation plugin installed
Tree View: Fixed inverted "Too many labels to display" warning
VCF Export: Added ability to export sequences as FASTA alongside VCF export
VCF Export: Fixed option to export original source being incorrectly enabled by default
VCF Import: Fixed source data files not being added correctly in some cases
UniProt: Fixed problem when search with multiple terms with a Match 'ALL' statement is returning results as Match 'ANY' statement
CSV/TSV Spreadsheet-Sequence importer: Fixed crash which happen in rare situations when importing document with CSV/TSV importer
Sequence Viewer Controls: Improved buttons to support larger font sizes and HiDPI displays
Annotation generator: Fixed memory leak caused by real time annotation generator progress bar

New in Geneious Prime 9.0.2 (Nov 4, 2015)

Bugs Fixes and Minor Changes:
Contig View: Trim annotations are now off by default on large contigs and reference mappings. When trim annotations are off, trimmed regions are shown as strikethrough text
Annotate from database: Includes annotations from tracks on sequences in database. Added option to only include specified annotation types. Added option to exclude specified annotation types.
RNA Seq / Structural Variant Mapping: The track created is now only visible by default on the contig it corresponds to and off when viewed from other contigs.
RNA Seq / Structural Variant Mapping: Fixed crashes in some situations
RNA Seq / Structural Variant Mapping: Fixed failure to run when 'Assemble each sequence list separately' is on.
MacOS and Linux: Fixed crash sometimes when out of file handles due to Geneious keeping too many files open
Info Viewer: Fixed incorrect error message about failure to save sometimes and crash soon afterwards
Fixed a crash that would occur if switching to the data storage location to a path ending in whitespace
VCF Importer: Changed the single sample naming scheme to use the imported file's name
32 bit operating systems: Fixed Geneious occasionally failing to start and/or occasionally crashing later during normal usage
Viewer preferences are now remembered when a new window is opened
Split views are now remembered when switching between documents of the same type
Extract PCR Product: Now correctly moves annotations in sequence tracks to account for any primer extensions
Set Paired Reads: When selecting multiple lists for batch pairing with variable length names, it now recognizes pairings when the forward/reverse variable character is before the last character and after the variable length position. e.g. A_1_F_001, A_1_R_001, A_2_F_001, A_2_R_001, A_10_F_001, A_10_R_001
Options dialogs: Basic options will have a scrollbar now and advanced (more) options will have appropriate size for better accessibility.
BBTools: Upgraded to version 35.49 and added PacBio mode checkbox to BBMap
Tree View: Expansion slider is now relative to the size of the tree so it can go high enough on huge trees and it stays consistent when switching between trees
Tree View: When there are more than 1,000 labels visible at once then they are all hidden to improve performance
Tree View: Many other improvements to rendering performance on huge trees
Geneious Server:
Removed SAMtools variant finder plugin from server. Uninstall the plugin from Geneious and use Geneious variant finder instead

New in Geneious Prime 9.0.1 (Nov 4, 2015)

Bugs Fixes and Minor Changes:
Map to Reference: Fixed crash with RNA seq or structural variant discovery in some cases
Map to Reference: When dissolving an existing contig and remapping, fixed 'Reads Name' assembly name property to correctly use the original reads name.
Map to Reference: Fixed occasional crash and occasional failure to map reads when sequencing reads are longer than a circular reference sequence. Long reads are now split into multiple fragments in the results.
Find Variants and Compare expression levels: Fixed very slow performance in some cases when calculating p-values.
Find Variants: Fixed crash merging adjacent variants when sequencing reads are longer than a circular reference sequence so that individual reads can contribute two different variants to a single position in the reference sequence
Contig Viewer: Trimmed regions when zoomed in with the paired distance color scheme and now rendered in grey
Workflows: When workflows create copies of sequences for their results, custom notes from the input sequences now appear on the output sequences
Workflows: Fixed occasional crash when changing your data location
Sequence Extraction: Genetic code is now copied from source sequence into extracted sequence
Contig/Alignment Viewer: Fixed complement rendering in wrong location if both complement and translation are turned on when translation is set to only show on consensus and/or reference sequences.
Sequence ligation: Ligating chromatograms with large sequences (over 100,000 bp) now discards chromatogram information from the results to prevent poor performance
Parts of a primer extension can now be removed via a delete button on each part
Extract PCR Product: Now retains annotations on primer extensions if you extract the primers from the pcr product
Extract PCR Product: Results now show original numbering on primer extensions relative to the extraction rather than the extensions themselves
Extract PCR Product: Fixed a bug where original numbering would not be set when the PCR product covered the whole sequence
Golden Gate: Extensions added to existing primers are no longer saved on original primer
Golden Gate: Improved parent descendant handling
Golden Gate: Fixed bug where it didn't update the vector correctly when some options were changed
Golden Gate: Adds enzyme annotation to extracted primers
Golden Gate: Added possibility to choose between multiple primers
Golden Gate: Update button is stateless and updates only when clicked
Mac OS: AppNap and sleep are now prevented when Geneious is running an analysis or importing or exporting (only on Mac OS 10.7+ with Java 8)
Large trees: Fix out of memory error when indexing large tree documents present in your database
Tree Viewer: Fixed bug where an options panel was disappearing whenever a tree was modified and saved
Tree Viewer: Fixed bug where autocollapse subtree options were not updating after re-rooting a tree
Tree Viewer: Fixed a bug where the tree view would freeze Geneious at certain zoom levels and auto collapse settings
Fixed a crash if Geneious could not create a new database on upgrade
CRISPR Site Finder: fixed bug that allowed it to annotate groups of Ns as valid CRISPR targets
BLAST: Fixed a bug where occassionally the full sequence was downloaded rather than just the specified hit context
Alignment: Fixed a problem where Geneious would hang when showing the options for re-aligning a large alignment
Start up: Fixed Geneious occasionally failing to start on 32 bit operating systems
Rename Folder: Fixed so that you can change the capitalisation of a folder name
VCF Importer: Fixed bug where multiple samples were being collapsed into one track

New in Geneious Prime 8.1.7 (Aug 11, 2015)

New in Geneious Prime 8.1.6 (Jun 18, 2015)

Bugs Fixed:
Modified Date: When editing documents, fixed bug where modified date would revert to the created date on some documents
Map to reference: Fixed iterative mapping causing reads to be mapped offset from where they should be in rare situations
Find Variants: For deletions over about 100bp, fixed incorrect average quality and p-values
Find Variants: Fixed bug where variants were not getting merged into longer variants sometimes
Find Variants: Fixed crash in some situations when working with RNA variants
Find Variants: Fixed crash when reference sequence has trimmed regions
Contig View: Hide columns over x% gaps would sometimes hide the wrong column in the right-most 8bp of the contig (the fix only applies to newly generated contigs)
Alignment View: Fixed 'Pairwise % Positive' value to ignore columns which are entirely gaps
BAM/SAM Export: Fixed so that template length (TLEN) in BAM/SAM files for right most paired read is negative
Blast2GO: Fixed crash when you have installed the Blast2GO plugin, created some results using Geneious, and then uninstalled the plugin
Shared Database / Custom BLAST: Fixed error message about data going missing when trying to view some custom BLAST results in a shared database
Shared Database: Stopped a crash that occurred when documents could not be cleared from the clipboard.
NCBI Gene DB: discontinued entries can be downloaded and won't be ignored anymore
NCBI Gene DB: Fixed failing downloads of entries with missing GenomicInfo
CRISPR Site finder: Added help button for inputting the CRISPR motif
UniVec: Updated the bundled UniVec database to the latest version
Gibson Assembly: Shows message that operation can't be performed when sequences are too short
Gibson Assembly: Fixed bug where it couldn't find some of the provided sequences in a sequence list
GenBank File Import: Fixed cases where fields were not imported if KEYWORDS didn't end with a period
GenBank File Export: Added option to export sequences with a LOCUS name longer than 16 characters

New in Geneious Prime 8.1.5 (May 4, 2015)

New in Geneious Prime 8.1.4 (Apr 8, 2015)

New in Geneious Prime 8.1.3 (Mar 17, 2015)

New in Geneious Prime 8.1.2 (Mar 3, 2015)

New in Geneious Prime 8.1.1 Beta (Feb 24, 2015)

Bugs Fixed:
Expression Analysis: Fixed crash when working with data sets where all reads map outside of CDS annotations
Sequence Viewer: Tweaked so that full names don't pop out until 0.5 seconds after you stop moving the mouse
Sequence Viewer: Fixed hang when editing lots of trim annotations
Sequence Viewer: Fixed hang when trimming lots of annotated sequences
Find Variants/SNPs: When run on multiple contigs, it now prompts whether or not to apply the changes to referenced documents
Find Variants/SNPs: Fixed so that merged variants which have a range of frequencies state the frequency range instead of just the maximum frequency
Find Variants/SNPs: Fixed so that merged variant frequencies aren't lower than expected when some reads only partially intersect the variant region
Find Variants/SNPs: Added "Variant Raw Frequency" property
Strip Alignment Columns: Fixed issue causing it to create inefficient alignments which would cause the alignment viewer to hang on large alignments
Contig Viewer: Fixed hang sometimes right clicking when a large region (100,000 + sequences) is selected
Contig Viewer: Fixed crash if you pick black as a paired distance color
Export: Fixed crash sometimes when exporting documents with parents and descendants
Export: Reduced size of Geneious format exported documents
Fixed crash sometimes working with over approximately 250 million paired reads
Biocode plugin: Fixed PCR plate primers going missing (bug introduced in 8.1.0)
RAxML, FastTree, Garli: Fixed crash shortly after running one of these for the first time
Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it.
Workflows: Fixed crash when running Filter workflow on multiple documents
Translation: Change translation of ambiguities (e.g. N) to translate as X instead of ?
Shutdown: Fixed hang sometimes when shutting down Geneious
Map to Reference: Tophat with Bowtie2 now accepts pre-built bt2 or bt21 index files
De Novo Assembly: No longer produces circular assemblies sometimes from contigs containing only two sequences
Lineage: Fixed so that lineage view includes documents selected by the new document chooser introduced in 8.1 for reference assembly, primer design and gibson cloning
Shared Database: Greatly improved start up time when the database has a lot of folders
Codon Optimisation: Removed incorrect message being displayed about no results being found
Codon Optimisation: Now optimises stop codons
Document Notes: Fixed failures when entering special characters

New in Geneious Prime 8.1.0 Beta (Feb 16, 2015)

New Plugins:
Blast2GO - All in one functional annotation tool and annotation data analysis.
FreeBayes - Haplotype-based variant detector for single sample analysis.
Efficient selection of reference sequences and vectors:
Store commonly used sequences such as reference genomes, vectors and biological parts in separate folders from your working data, then easily choose them when you run Map to Reference or Gibson Assembly.
Sort by GC Content:
All newly created nucleotide alignments, contigs, sequence lists, and sequences have a %GC field in the document table. Sequences in alignments, contigs and lists can be sorted by %GC.
Improved Primer Design for qPCR:
Batch design primers for many regions within a single sequence in one step, great for qPCR design. Primer design and testing now have an option to match each sequence in an alignment (instead of just the consensus).
Mapping Qualities now included:
Geneious mapper produces mapping qualities, SAM/BAM import/export handles mapping qualities, contig viewer displays mapping quality in status bar, added mapping quality color scheme.
Integration with LIMS and external web-based systems:
Geneious documents can now be opened by clicking a link in external web-based systems.
Easier Exporting for Newick and FASTA formats:
Documents can now be exported in the compressed .fasta.gz and .fastq.gz formats. Export Tree documents: Export to newick format may now include bootstrap support values.
Molecular Cloning and Primer Design:
Batch Primer Design: Design primers for many regions within a single sequence in one step.
Vectors and inserts can now be chosen from different folders after opening "Gibson Assembly"
Primer design and testing now have an option to match each sequence in an alignment (instead of just the consensus)
CRISPR Design: Locate potential CRISPR target sites using innovative heatmap-style annotations to assess sites based on off-target interaction.
Refine your search for restriction sites by methylation sensitivity.
Added support for use of inosine (I) bases in primers
Greater control of degenerate primer design by specifying consensus options
Alignment, Assembly and Mapping:
Contig/Alignment Viewer: Added option to only show translation on consensus and reference sequences
All newly created nucleotide alignments, contigs, sequence lists, and sequences have a %GC field in the document table. Sequences in alignments, contigs and lists can be sorted by %GC
Reference sequence can now be chosen from a different folder after opening "Map to Reference"
Mapping Qualities: Geneious mapper produces mapping qualities, SAM/BAM import/export handles mapping qualities, contig viewer displays mapping quality in status bar, added mapping quality color scheme, variant finder takes mapping qualities into account when calculating variant p-values
De novo assembly and map to reference: Better results on data with gappy error models (e.g. Ion Torrent data)
Sequence Viewer: Added checkbox to 'find in sequence' dialog to disable finding the reverse complement too
Improved NGS Assembly: Scaffolding, longer contigs, greater accuracy
Generate Consensus: Added option to split consensus into multiple sequences around regions of no (or low) coverage
Reverse complement individual sequences within alignments and contigs
Move reads mapped to a reference sequence to a specific position in the contig
When coloring by paired distance unpaired forward directed and reverse directed reads are assigned distinct colors
New Plugins:
Blast2GO PRO Plugin for functional annotation
FreeBayes Variant Finder Plugin (64 bit platforms only)
CRT (by Chris Duran) Identifies existing known CRISPR sites in bacteria and archaea
FLASH (by Dave O’Connor)- Merge paired sequencing reads using FLASH
SeqPartitioner (by Jed Barlow) - Partition allele multisets from multiple alignments
Augustus (by Michael Thon) Predict genes using the Augustus algorithm.
EMBOSS Nucleotide Analysis (previously bundled) Search for transcription factors, and predict protein coding regions.
EMBOSS Protein Analysis (previously bundled) Predict secondary structure, antigenic regions and signal cleavage sites
Go To Documents - Jump to documents by entering their unique IDs
Find Big Folders Workflow - List the size of all folders in your local database
Groovy Console - List the size of all folders in your local database
Data Organization:
Export Documents: Documents can now be exported in the compressed .fasta.gz and .fastq.gz formats
Export Tree documents: Export to newick format may now include supporting values
Import speed and memory usage has been improved for very large trees
Shared Database: Admin users can now specify a compatibility version that will determine the format used to save documents in the database.
Geneious documents and files can now be opened by clicking a link in web-based systems (Windows and Mac OS only) - see Administration section in user manual
Sequence Analysis and Annotation:
Compare Expression Levels: Added log ratio, normalized transcript counts, and normalized TPM as properties for each gene
Annotations Table: Added a right click popup menu to allow copying the selected value, extracting, translating, showing on sequence, editing, and deleting
16S Biodiversity Tool: A cloud-based tool that identifies high-throughput 16S rRNA amplicons from environmental samples using the RDP database, and visualizes biodiversity as interactive graphs and charts using a secure web viewer.
Sequence Classifier Plugin: Taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST-like algorithm with multiple loci and trees to assist with identification.
Features:
Batch Primer Design: Design primers for many regions within a single sequence in one step.
Vectors and inserts can now be chosen from different folders after opening "Gibson Assembly"
Reference sequence can now be chosen from a different folder after opening "Map to Reference"
FreeBayes Variant Finder Plugin (64 bit platforms only)
Contig/Alignment Viewer: Added option to only show translation on consensus and reference sequences
%GC: All newly created nucleotide alignments, contigs, sequence lists, and sequences have a %GC field in the document table. Sequences in alignments, contigs and lists can be sorted by %GC
Mapping Qualities: Geneious mapper produces mapping qualities, SAM/BAM import/export handles mapping qualities, contig viewer displays mapping quality in status bar, added mapping quality color scheme, variant finder takes mapping qualities into account when calculating variant p-values
Export Documents: Documents can now be exported in the compressed .fasta.gz and .fastq.gz formats
Export Tree documents: Export to newick format may now include supporting values
Import speed and memory usage has been improved for very large trees
Shared Database: Admin users can now specify a compatibility version that will determine the format used to save documents in the database.
Geneious documents and files can now be opened by clicking a link in web-based systems (Windows and Mac OS only) - see Administration section in user manual
Minor Features:
Compare Expression Levels: Added log ratio, normalized transcript counts, and normalized TPM as properties for each gene
Sequence Viewer: Added checkbox to 'find in sequence' dialog to disable finding the reverse complement too
Primer design and testing now have an option to match each sequence in an alignment (instead of just the consensus)
De novo assembly and map to reference: Better results on data with gappy error models (e.g. Ion Torrent data)
Annotations Table: Added a right click popup menu to allow copying the selected value, extracting, translating, showing on sequence, editing, and deleting
Bugs Fixed and Minor Changes:
Windows: Double clicking '.geneious' files now opens them in Geneious
Fixed bug that wrongly allowed creation of contigs containing a single sequence, which could lead to later crashes
Improved performance working with databases with thousands of folders
Improved performance when running low on available memory
Group Sequences and Extract Sequences: Fixed so that edited field values (e.g. taxonomy) on the source document are correct on the derived document
Workflows: Fixed translation operation in workflows to translate in frame 1 instead of frame 3
BAM Import: Fixed excessive memory use and poor performance importing bam files with long reads
BAM Import: Imports mapped reads without sequence data as a sequence of ambiguous nucleotides (NNN...)
BAM Import: Fixed crash when importing corrupt BAM files
BAM Export: Uses read group names with spaces replaced with underscores since some other software can't handle spaces in read group names
BAM Export: No longer replaces IUPAC ambiguity symbols with N, but also added an advanced option to enable the old behaviour
De Novo Assembly: 'Use x % of data' setting can now specify values less than 1%
De Novo Assembly: Stopped it producing circular scaffolds sometimes when the circular assembly setting is off
De Novo Assembly: Fixed crash in rare situations when producing scaffolded circular contigs
Wrapper plugins: Added debugging mode to see the exact command being run
Wrapper plugins: Report progress when importing large results
Wrapper plugins: Fixed so that help window isn't hidden behind the wrapper plugin window
Wrapper plugins: Fixed so that it doesn't crash when attempting to import invalid result files into Geneious
Primer Editing: Fixed crash when attempting to remove the interval from a primer annotation
Sequence Viewer: Fixed bug when double clicking the ends of an annotation when in editing mode prompts to edit the annotation twice
Sequence Viewer: Fixed out of memory crash when 'Find All' finds too many results
Sequence Viewer: Fixed crash sometimes when deleting annotations outside the bounds of the sequence
Sequence Viewer: Fixed crash when doing a 'Find' while dragging regions or annotations around
Sequence Viewer: Improved performance viewing intersecting CDS annotations
Sequence Viewer: Displays translation for every region covered by a CDS annotation instead of not showing translation at all for CDS annotations that intersect other CDS annotations
Sequence Viewer: Fixed rendering glitches on large circular sequences
Sequence Viewer: Improved performance and reduced memory usage when viewing lots of sequences (e.g. 100,000 +) extracted as sub-sequences
Sequence Viewer: Fixed excessive memory usage and improved performance when saving large tracks
Sequence Viewer: Fixed crash adding annotations to sequences with trim annotations when the complement strand is visible
Sequence Viewer: Fixed crash changing annotations outside the sequence bounds into primer annotations
Contig/Alignment Viewer: Fixed hang / poor performance viewing larges contigs that have CDS annotations on the consensus sequence
Contig/Alignment Viewer: Fixed hang / poor performance viewing translation in frame of consensus on sequences with large gaps
Contig/Alignment Viewer: Fixed hang / poor performance extending selection with shift-up/down arrow keys
Contig/Alignment Viewer: Fixed copying text to clipboard on circular contigs which would sometimes copy gaps instead of the selected nucleotides
Contig/Alignment Viewer: Fixed crash in rare situations when editing contigs with trimmed sequences
Contig/Alignment Viewer: Fixed crash exporting coverage graph from circular contigs
Contig/Alignment Viewer: Fixed crash or incorrect paired read handling extracting from a contig when the consensus is also selected
Enzymes Viewer: Disabled on over 100,000 sequences to prevent hangs
Primer Design: Fixed some crashes on circular sequences when entering an invalid included region
Conflicting Changes: Fixed rare message about there being conflicting changes when saving a document when there aren't any conflicts
Digestion Operations: Fixed a possible hang when thousands of sequences should be digested
VCF Import: Fixed so that meta info and some annotation properties are not discarded in some cases
Reverse Complement: Fixed crash in rare situations when clicking the 'Reverse Complement' button
Gibson Assembly: Replace 'Editing History' with 'Gibson Primer Extension' annotation to include it in primer extension
Gibson Assembly: Using a new document chooser that can remember previously selected vectors
Custom Blast: Corrected handling of preformatted & custom Blast databases
Custom Blast: Naming & Accession of Local Blast Hits was sometimes incorrect
Custom Blast: Summaries from workflow can now download the full sequence from its original service
Dropbox: Fixed crash when you have partially synchronized your data with Dropbox and DropBox has created "conflicted copy" files in your Geneious database. Using Dropbox like this can lead to data loss so we strongly advise against using it.
Expression Analysis: Fixed crash sometimes when running two expression analysis operations simultaneously on the same reference sequences
Fixed a crash that can occur when the data folder is the root of a hard drive and the user upgrades their Geneious version
Annotate From and Transfer Annotations: transferred primer annotations are now named for the primer they came from, and include extension information
Annotate From: Multiple primers with different extensions are transferred as separate annotations, instead of merged into one annotation
Restriction Enzyme Finder: Disabled unnecessary & buggy range option on multiple unaligned sequences
Set Paired Reads: Pairing multiple data sets with variable length document names now works (e.g. sample1_R1, sample1_R2, sample2_R1, sample2_R2, ..., sample10_R1, sample10_R2)
Genome Summaries: Downloads always the newest version
Tree Building: Fixed crash in some cases when building trees from sequences with duplicate names
Import tree documents: Fixed a Bug where imported unrooted newick trees might have had the supporting values on the wrong branch
Create tree documents: Fixed a Bug that might happen when Taxa were named as integer smaller than the total amount of taxa
Plugin Download: Fixed performance issue so that plugins now download and install faster
Blast Hits: correct representation of transferred annotations in alignment and query centric view
Other Notes:
"Download Annotation Tracks" has been removed due to incompatible changes to the data at the Broad Institute

New in Geneious Prime 8.0.5 (Dec 10, 2014)

New in Geneious Prime 8.0.4 (Nov 3, 2014)

New in Geneious Prime 8.0.3 (Oct 22, 2014)

New in Geneious Prime 8.0.2 (Oct 7, 2014)

New in Geneious Prime 8.0.1 (Oct 7, 2014)

FEATURES:
Basic RNA-Seq statistics: Added operation to calculate RPKM, FPKM, and TPM
Basic RNA-Seq differential expression: Added operation to calculate differential expression between two samples
CRISPR Site Finder: Added option to find and score paired sites on opposite strands
Sequence Viewer: Added "Invert Selection" (available from right click menu)
Tree Viewer: The reference sequence is highlighted in green and not hidden when there are too many labels to show them all
BUGS FIXED:
MIRA: Fixed crash when turning off the option to save contigs
Garli: Fixed failure to run when sequence names contain unusual characters
RAxML and other tree builders: Fixed crash on some data sets
Contig Viewer: Fixed crash setting reference sequence on a circular contig
Contig Viewer: Fixed poor performance / out of memory when viewing lots of sequences with CDS annotations mapped to a reference sequence
Contig Viewer: Fixed crash when running low on memory
Tree Building: Trees built from alignments with a reference sequence keep the reference sequence in the tree
Sequence Viewer: Fixed so that it highlights the correct sequence as reference sequence on tree documents
Sequence Viewer: Fixed poor performance / hangs viewing lots of ORF annotations on MacOS
Sequence Viewer: Fixed crash when attempting to edit a sequence that has unsaved changes in a separate window
Sequence Viewer: Fixed crash sometimes when exporting graphs
Sequence Viewer: Fixed incorrect codon usage statistics when there are overlapping CDS annotations
Sequence Viewer: Fixed incorrect translations when there are truncated CDS annotations
Sequence Viewer: Fixed occasional crash when clicking the mouse
Sequence Viewer: Fixed circular sequences being displayed as linear with default settings when upgrading from 7.1 to 8.0.0
Annotations Table: Fixed to correctly display properties that have html contents
Tutorial Document Importer: Preserves the folder structure of the imported tutorial zip file
Distances viewer: Fixed it incorrectly reporting 100% identity when two sequences had the same name
Workflows: Strip alignment columns is now configurable from workflows
Workflows: Fixed translation operation creating duplicate sequences when used on multiple sequence lists. And improved name of documents produced
Map to reference: Fixed crash when using 'Only map reads which match nearby'
Map to reference: Fixed crash when mapping large sequences from genbank
Custom BLAST: Fixed crash when adding large sequences from genbank to a custom database
Export: Fixed crash when exporting MrBayes documents in Geneious 6.0 format when the MrBayes plugin is not currently installed
Cloning: Fixed crash in some situations when forwarding changes to descendants of genbank sequences
Primer Trimming: Stopped it wrongly finding results with single mismatches when 'Allow Mismatches' is off
Meta-data: Fixed issue where large amounts of text would cause Geneious to freeze
Removed link to order Primers from Eurofins MWG Operon in Text View of oligo sequences

New in Geneious Prime 8.0 (Oct 7, 2014)

FEATURES:
16S Biodiversity Tool - Cloud-based tool that identifies high-throughput 16s rRNA amplicons from environmental samples using the RDP database, and visualizes biodiversity as interactive graphs and charts using a secure web viewer
Sequence Classifier - Taxonomically classifies an organic sample by how similar its DNA is to your own database of known sequences using a BLAST-like algorithm with multiple loci and trees to assist with identification (available as a separate plugin)
CRISPR Design - Locate potential CRISPR target sites and score them based on off-target sites in any genome
Improved De Novo Assembly - Longer contig lengths, more accurate results, and can also produce scaffolds
Genetic Codes: Added support for defining your own custom genetic codes (from the cog icon next to the genetic code in the sequence viewer)
Generate Consensus: Added option to split consensus into multiple sequences around regions of no (or low) coverage
Sequence Viewer: Select some of the annotation results from Live Annotate & Predict before clicking Apply to have only those annotations applied
Sequence viewer: Added advanced option in preferences to allow displaying more annotations at once (warning: this can cause poor performance)
Primer Design: Added Inosine (I) to allowed nucleotides
Windows / Linux: Added option to let Geneious automatically choose a reasonable amount of memory to use based on your machine's total memory.
When copying documents between folders there is now an option to "keep both" when a document with the same name exists
Restriction Analysis:
Methylation sensitivity now listed for all enzymes
Added "Must cut between: (may cut outside)" option when finding restriction sites
Enzyme list is now automatically updated from rebase
Workflows:
Merge overlapping sequences mapped to a reference as long as the overlap size and similarity meet specified thresholds (useful for genome finishing)
Custom code workflow for extracting sequences from a list or alignment by name
Split a sequence list into smaller sequence lists
Add a translation property to all CDS annotations
New workflow step to extract the reference sequence from contigs or alignments
Contig Viewing:
Added option to reverse complement individual sequences within contigs
Added option to move reads mapped to a reference sequence to a specific position in the contig
When coloring by paired distance unpaired forward directed and reverse directed reads are assigned distinct colors
BUGS FIXED:
Fixed slow shutdown of Geneious when a large document is being indexed
Alignment Editing: Fixed deletion of wrong nucleotide in rare situations when you have the cursor positioned in multiple positions in multiple sequences and press shift-backspace
Workflows: Fixed so that when operations which save to a sub folder are part of a workflow, they still save to a sub-folder
Workflows: Find ORFs 'Continue outside sequence' option is now available from workflows
Workflows: Find Duplicates is now configurable from workflows
Workflows/Shared Database: Fixed crash on startup in rare situations when workflows are stored in shared databases
Mapping: Fixed crash mapping to a 0 length circular reference sequences
Mapping: In some cases gaps near mismatches would be positioned differently for different reads when they could be placed in multiple locations with the same number of mismatches. Now gaps are always positioned as far right as possible
Sequence Viewer: Fixed poor performance when viewing thousands of unaligned sequences with annotations
Sequence Viewer: Fixed poor performance / hangs when creating or saving non-trim annotations on large sequence lists
Sequence Viewer: When finding sequences that occur in millions of locations, warns you before running out of memory or hanging/li>
Sequence Viewer: Fixed crash when extracting from sequences with large tracks when running low on memory
Sequence Viewer: Fixed circular sequences with over 500 annotations turned on, so that it now shows annotations spanning the origin when zoomed in
Sequence Viewer: Improved performance on MacOS and also fixed occasional hang on MacOS
Sequence Viewer: Fixed poor performance / hangs when a large quantity of text (e.g. 10MB or more) is copied to the clipboard in other applications
Sequence Viewer: Fixed crash when there are hundreds of different types of annotations on a sequence
Sequence Viewer: Fixed hang/crash when translating a large list of sequences in all 6 frames
Sequence Viewer: Fixed bug with circular sequence viewer that wasn't always positioning the cursor correctly when running Geneious with Java 8
Sequence Viewer: Fixed rare crash when drag selecting regions
Sequence Viewer: Fixed rare crash view sequence list documents with translation turned on
Sequence Viewer: Fixed rare crash copying selection to clipboard
Sequence Viewer: Fixed crash after editing multiple annotations in tracks
Sequence Viewer: Fixed crash deleting lots of selected regions from sequences
Sequence Viewer: Fixed crash and/or incorrect coloring of heat mapped annotation tracks after manually editing an annotation
Sequence Viewer: Fixed crash and/or incorrect results after renaming a newly generated track and using the undo button
Sequence Viewer: GC% being lower than it should be due to gaps and ambiguities being counted as non-GC characters
Sequence Viewer: Fixed poor performance / hangs when viewing large sequence lists containing circular sequences
Alignment Viewer: Fixed rare crash when extracting sequences from an alignment
Contig Viewer: Fixed poor performance / hangs when dragging regions of sequences around in large contigs
Contig Viewer: Fixed poor performance / hangs when copy annotations to all sequences in a large contig
Contig Viewer: Fixed out of memory / poor performance / hangs / when turning off nucleotides and names on high coverage contigs
Contig Viewer: Fixed ugly rendering of consensus sequence when mouse is over the sequence name
Annotations: Fixed various case sensitivity issues. For example when editing annotation types. And when finding variants where 'cds' annotations were not recognized as 'CDS' annotations
Annotations Table: The 'Sequence' column for primer annotations shows the primer sequence instead of the region covered by the primer
Annotations Table: Fixed crash on MacOS sometimes when editing annotations
Find Variations/SNPs: Fixed crash when ignoring SNPs in annotations that have intervals outside the sequence range
Extract Annotations: Fixed poor performance and excessive memory usage on large contigs
Separate by barcode: Fixed out of memory error when separating into hundreds of barcodes each of which has thousands of sequences
Windows: Fixed crash that can happen when changing Windows theme (or in other situations involving display changes)
Windows: When installed from the MSI, a running instance of Geneious can be pinned to the taskbar on Windows 7 and Windows 8.1
Dotplot viewer: fixed problem with lines getting thinner and thinner until they almost disappeared as you zoomed out
Text View: Fixed crash sometimes when selecting documents
Import: Fixed crash sometimes when importing multiple files when one of the files is unable to be imported
Import: Fixed crash when auto determining the file format of a very large file
Import: Fixed crash when trying to import a compressed empty file
Nexus Import: Fixed crash when importing deep nexus trees
SAM/BAM Import and bowtie running: Stopped Geneious prompting about the sequence type when the reference sequence contains too many ambiguities
BAM Import: Fixed crash when attempting to import corrupt BAM files
RAxML: Now works if sequence names contain characters such as brackets
Group Sequences: Fixed some document types (such as primers) from losing their document type when grouped and extracted again
Group Sequences: Preserve paired read information when grouping multiple lists together
Fixed invalid primer type in sample documents
Extract PCR Product: new documents get the name of the sequences they were extracted from rather than the name of the sequence list or alignment
Fixed extension options in primer design not remembering their values
Fix for the deletion of associated annotations
Primer design on alignments: Now exposes the sequence viewer's consensus options for more fine-tuned control of the consensus
When deleting a primer annotation in a sequence list or alignment, the associated annotations can also be deleted now
Custom Blast now downloads full hits from the NCBI database if no local database is available
Fixed crash when out of disk space
Fixed crash on startup when system temporary directory property is invalid
Batch rename: Fixed a bug where renaming empty strings as part of a larger pattern wasn't working.
Genbank exporter no longer creates a blank version field (which caused BioJava to fail)
Made it easier to track down documents that are causing indexing to fail on a shared database
OTHER NOTES:
UniVec has been updated
COGs BLAST has been removed
Linnaeus Search has been removed
NCBI Genome service now uses BioProjects to retrieve sequences
64-bit versions of EMBOSS tools have been added which includes the dotplot, motif search and back translation
Three protein analysis tools have been moved to a separate downloadable plugin called "EMBOSS Protein Analysis": Predict Secondary Structure, Predict Antigenic Regions, Predict Signal Cleavage Sites
Two DNA analysis tools have been moved to a separate downloadable plugin called "EMBOSS Nucleotide Analysis": Search for Transcription Factors, Protein Coding Prediction Graph
Generate Mutated and Shuffled Sequence operations have been moved to a separate downloadable plugin called "Mutate & Shuffle"
Genetic Codes: Added NCBI tables 24 and 25
Stylized DNA Helix Graph: Added option to stop the animation
Sequence viewer: "Linear view" option moved to the General options tab

New in Geneious Prime 7.1.7 (Jul 30, 2014)

New in Geneious Prime 7.1.6 (Jul 15, 2014)

Sequence Viewer: Fixed hang sometimes when saving changes
Contig Viewer: Fixed poor performance on high coverage contigs when consensus numbering is on
Map to Reference: Fixed selected sequence lists not showing up as available reference sequences in some situations
Variant Finder: In regions of overlapping CDS annotations, fixed some variants not being found on the 2nd CDS annotation in some situations where an adjacent variant is also present.
SAM/BAM import: Fixed crash importing files where the reference sequence name in the SAM/BAM file includes the '.fasta' extension
SAM/BAM import: Fixed crash sometimes importing files when selecting only one of the potential reference sequences and importing to blank sequences for the others.
SAM/BAM export: Fixed crash and/or failure to export when exporting multiple contigs
Fixed a bug where users would get a crash on startup trying to load windows native libraries. Previously thought to be fixed, but wasn't.
Genbank Exporter: fixed an issue where importing and reexporting a file to genbank flat and xml format would lose some of the Geneious-specific information associated with the annotations.
Genbank Exporter: updated the list of qualifiers and feature types, which was out of date.
Export: Fixed non-ascii characters (e.g. Greek characters) not appearing correctly in exported files on Windows
Export Graphs: Transposed csv so that each row (instead of column) represents a single position in the sequence or alignment (this means large files can now be imported into Excel)
Annotate from database: Fixed bug causing only the best result for near-duplicates to be annotated sometimes instead of annotating all matching locations
Annotate from database: Removed near-duplicates being annotated over the same region as a better match
Annotate from database: Displays the range of similarity scores instead of just the best one contributing to an annotation that is obtained from multiple sources
Transfer annotations: Fixed calculated similarity scores being lower than they should have been
Fixed an issue with the Vector NTI importer failing to link some parent descendent documents

New in Geneious Prime 7.1.5 (May 15, 2014)

SAM/BAM Import: Fixed incorrect estimate of paired read insert size when there are unmapped reads present
Export: Fixed crash when exporting some sequence search results in a format compatible with Geneious 6.0
Fixed occasional crash when clicking on a folder
Batch Rename: Fixed crash that could happen in rare cases when renaming lots of documents
Shared Database: Fixed an issue preventing documents larger than 2 GB from being loaded when stored in a PostgreSQL v9.3 database
Shared Database: Fixed an error that prevented document history from being imported from .geneious files when using certain MySQL versions.
Cloning: Fixed a bug where Multicassette reactions would crash when a document's Att annotations' names had been changed from their defaults
Sequence Viewer: Fixed poor performance / hangs when annotating results of "Find All" when there are over 10,000 regions
Sequence Viewer: Turned on 'Create separate annotation for each interval' option by default since having this off causes performance issues when a single annotation has thousands of intervals
Sequence Viewer: Fixed crash in rare cases when slow running 'Annotate & Predict' results come back after you unselect the document you ran it on
Sequence Viewer: Fixed alignment data becoming incorrect in some situations when a sequence list it references has sequences deleted or reordered
Alignment Viewer: Fixed very poor performance calculating statistics on large protein alignments which could lead to out of memory errors
Installation: Fixed failure to run when installed to a location that contains a plus sign in the folder name
NCBI: Fixed a bug where some WGS result documents would crash
NCBI: Fixed a bug where Sequence Search would crash when run on certain 3D structure documents
MIRA Assembler: Fixed out of memory error caused by excessive information messages from MIRA going into the assembly report
Primer design: Fixed a hang in the results dialog that could happen when Map Primers was run on a large sequence list, improved the dialog's usefulness
Nexus export: increased speed when exporting large alignments as interleaved Nexus
Genbank flat export: fixed issue with identifier that ends exactly at linebreak
BLAST: default URL changed
Import: Fix crash whe auto determining the file format of a very large file
Geneious Server:
Patch a bug in Tomcat 6 introduced by a security update from Red Hat that breaks Geneious Server

New in Geneious Prime 7.1.4 (Apr 16, 2014)

New in Geneious Prime 7.1.3 (Mar 21, 2014)

New in Geneious Prime 7.1.2 (Mar 5, 2014)

New in Geneious Prime 7.1.1 (Mar 5, 2014)

Workflows: Fixed crash and/or incorrect results when running trimming workflows on data sets of over 100 sequences
Sequence Viewer: Fixed status bar displaying the incorrect number of results when running some 'Annotate & Predict' operations (e.g. trimming)
Sequence Viewer: Now includes annotations between bases that are directly on the end of extracted regions in the extraction (also applies when propagating changes from alignments to referenced sequences)
Sequence Viewer: Fixed poor performance when saving changes to some alignments/contigs
Sequence Viewer: When showing the "Bin" field next to the sequence names, the html tags are removed
Sequence Viewer: Fixed crash when extracting sequences from an alignment after reordering the sequences
Sequence Viewer: Fixed crash in rare situations when saving changes to contigs containing chromatograms
Sequence Viewer: Fixed translation by consensus to include translation of sequences that have insertions relative to the consensus
Sequence Viewer: Fixed hang when finding all occurrences of a very common motif when 'translate by selection' is on
Insert Sizes Graph: Fixed incorrect results on short contigs
Compare Annotations: Added trio analysis option to find for example annotations in both sets A and set B, but not set C
Workflows: Fixed batch rename always renaming the 'Name' field instead of the chosen field when run from workflows.
Primer Editing: Fixed crash when editing primers pairs so that they overlap each other
Primer Editing: Fixed crash when editing a primer binding site to lie outside the current binding range
Sequence Search: Handled an exception caused by Genbank returning data of the wrong type
Document Table: Fixed occasional crash and/or columns in document table not correctly saving the most recent position and size sometimes
Startup: Fixed Geneious saying your data location isn't writable if it had failed to write to it during an earlier attempt when out of disk space
Startup: Fixed crash if you cancel backing up your data when upgrading Geneious
Startup: Fixed warnings about missing plugin files on Mac OS when starting Geneious from network drive
Preferences: Fixed preferences getting wiped on shutdown in rare situations
SAM/BAM Import: Fixed crash when importing some documents
Genome Search: Returns all genomic sequences from RefSeq that are linked to the organism(s) the search term is related to
CAF Importer: Added support for paired reads
CAF Importer: Fixed importing trim-annotations
DNAStar Importer: Fixed a bug where it would import invalid characters when importing from Genbank-style format sometimes.
Primer Design: Fixed a crash when trying to design characteristics for an extremely degenerate primer
Primer Testing: Fixed crash when testing on some alignments
Batch Rename: Fixed a crash renaming the Description field on Sequence List Documents' individual sequences
Translate Sequences: Fixed a bug where a translation of multiple annotations with several intervals was sorted in reverse order

New in Geneious Prime 7.1 (Mar 5, 2014)

De novo assembly: Added option to produce circular contigs when the ends match
De novo assembly: Better results on data with gappy error models (e.g. IonTorrent or 454 data)
De novo assembly: Reduced size and improved performance on large lists of consensus sequences produced
Strip Alignment Columns: Add an option to remove columns that contain at least one ambiguity
Strip Alignment Columns: Add an option to strip two columns per codon
Extract Annotations: Added options to include upstream, downstream and intergenic regions of matching annotations
Compare Annotations: Easier to use interface, better results, more powerful options (including 3 way comparison), and results include annotation properties
Statistics: Added molecular weight of short nucleotide sequences
Primers can now be ordered from Eurofins MWG Operon via link on the Text View of oligo sequences
Alignment Viewer: Added option to number bases in the consensus sequence
Sequence Viewer: Improved performance when scrolling with the mouse wheel
Sequence Viewer: Displays the name of the track which an annotation is in the popup text when hovering over an annotation
Shared Database: Added the ability to set the group for new folders to be inherited from the parent folder in addition to the user's primary group
SAM/BAM importer: Improved performance
Tutorials: Import into a sub-folder instead of putting all the files directly in the folder they are dragged into
Identify Organism Workflow: It also includes the taxonomy fields (where available) on each sequences identified
Distance matrix: Decimal places option is not available for similarity
Primer testing: now works on the consensus (in a similar way to designing) when run on alignments and contigs
General performance improvements
Bugs fixed:
Read Mapping: Better results in some cases and fixed rare crash when mapping to a circular reference sequence
Info Properties Viewer: Long values wrap to the next line instead of disappearing off the right hand side of the view
Alignment Viewer: Fixed crash when saving after changing the genetic code on non-editable alignments
Sequence Viewer: Fixed poor performance rendering translation when there are translation annotations with lots of short intervals
Sequence Viewer: Fixed crash sometimes when opening sequence with tracks on it in a new window
Sequence Viewer: Fixed consensus sequence being assigned quality differently than how the consensus operation assigned quality around homopolymer regions
Newick Export: Exports multiple bootstrap trees instead of just the first one
SAM/BAM Import: Fixed failure to import some files which have padded alignments
Assemble by name: Fixed excessive memory usage leading to out of memory error
NCBI Blast: Fixed crash when binning into has hit vs no hit when run on sequences in alignments
Read Mapping: Fixed tracks on input reads not appearing in output contig when mapping to all matching locations
MUSCLE alignment: Update MUSCLE to version 3.8.425 which fixes problems aligning a long sequence
Annotation editing: Fixed crash when editing annotations on 0 length sequences
Annotation filtering: Fixed not equals (!=) clause giving incorrect results
Internet connection: Switched Geneious to prefer ipv4 to fix internet connection issues encountered by people whose firewalls, virus scanners, or proxy servers don't support ipv6
Annotate From and Transfer Annotations: 'Translation' properties on the source annotations are removed and replaced with a 'Transferred Translation' property
Annotate From: Fixed documents becoming excessively large when iteratively transferring annotations by using newly annotated sequences as source sequences for future annotation
Consensus Alignment: Fixed crash if document is modified while alignment is in progress
Consensus Alignment: Fixed crash sometimes when run on mixture of alignments and stand-alone sequences
Variant Finder: If find variants is run when there were unsaved changes on a small contig with paired reads, variants near the ends of the contig were wrongly filtered out due to strand bias
Extracting sequences: If an identical annotation is present in multiple tracks, it would only appear in one of the tracks in the extracted sequence
Performance: Fixed occasional hangs and poor performance when local documents contains 100,000+ documents
Workflows: Fixed failure to compile custom code workflows after Geneious had crashed or locked up earlier.
Workflows: Fixed crash on some documents when using the 'Filter Documents' workflow step
VCF importer: Properly support missing data fields
Annotations Table: Fixed crash sometimes when selecting multiple contig documents
Extract Annotations: Fixed a bug where the option to only include contained annotations wasn't working correctly.
Fixed occasional crashes that can happen at any time while Geneious is checking if any new plugins are available.
Fixed occasional crashes when working with folders with hundreds of documents in them
Custom Blast: Fixed a bug where Custom BLAST databases could get into a corrupt state if deleted during blast operations.
Custom Blast: Fixed crash when working with Custom BLAST databases that contain invalid nucleotides in the fasta file
Network drives: Fixed crash and improved performance if data location is set to a network drive
Backup: Fixed poor performance when backing up to a network drive (poor performance was introduced in 7.0.5)

New in Geneious Prime 7.0.6 (Dec 16, 2013)

New in Geneious Prime 7.0.5 (Nov 26, 2013)

Sequence Viewer: Turned off the new 7.0 feature where edited bases are bold and the red squiggle for deleted bases because it was annoying in some situations. It can now be enabled from the editing annotation type popup menu.
Sequence Viewer: Fixed crash sometimes when open a document in a new window
Sequence Viewer: Fixed crash when choosing to edit all annotations of a particular type when there is only one annotation of that type
Generate Consensus Sequence Operation: Stopped it wrongly using 'Highest Quality' on protein alignments
Download Annotation Tracks: Fixed crash downloading some tracks, and fixed empty additional tracks which sometimes appear
Fixed poor startup performance when 'Deleted Items' contains lots of documents
Custom BLAST: Fix memory leak of open file handles which could Geneious to crash during or after using custom BLAST
Chromatograms: Fixed crash in some situations when extracting or sequence searching from them
Backup: Fixed problems when out of disk space during backup
Backup: Made backup write directly to the backup drive instead of a temp file on the Geneious data drive first
Sequence Search: Fixed crash after deleting sequences from a sequence list which was previously used as input to a sequence search
SAM/BAM import: Fixed reads being paired with the wrong mate when importing some files
Extract Annotations: Fixed crash in some cases when extracting entire sequences from alignments
3-D structure view: Fixed selection being offset from correct selection on some rare types of documents
Import/Export on Linux: Fixed file selection problem in Import and Export file chooser dialog in Linux that could cause display error or a crash
Batch rename: fixed a bug where types of documents with a custom field named "name" wouldn't be able to be renamed
Primer design: fixed a bug where designing primers with certain target region/included region combinations on alignments would fail
Primer design: clarified the expected format of the a custom mispriming library file
Primer design: fixed bug where designed primers were being thrown away prematurely based on degeneracy
Sequence Search/NCBI/Transfer annotations: fixed an issue in rare cases on translation searches where a "original sequences were modified" message would pop up. Transfer annotations would also fail.
NCBI: Fixed a bug where some full sequences from certain protein summary documents would not download
Geneious Server:
No longer require the home directory of the Geneious Server HOSTNAME linux account to be /home/HOSTNAME

New in Geneious Prime 7.0.4 (Oct 31, 2013)

New in Geneious Prime 7.0.3 (Oct 16, 2013)

New in Geneious Prime 7.0.2 (Oct 8, 2013)

Contig Viewer: Fixed crash sometimes when turning on 'Vertically Compress Contig'
Contig Viewer: Added option to sort by read direction
Sequence Viewer: Fixed names of sequences being incorrectly truncated sometimes
Sequence Viewer: Can use annotation properties of annotations in tracks as the displayed label for that annotation type
Sequence Viewer: Fixed setting sequences to circular on some sequence lists not working.
Sequence Viewer: Fixed poor performance and results being skipped sometimes when pressing enter to jump through filter matches
Sequence Viewer: Removed some unused annotation types from the annotation type drop down list and increased the scrollable region height
Sequence Viewer: Fixed crash occasionally when editing primers
SamTools Variant Finder (Geneious Server): Fixed it not working when run from Contig Viewer's 'Annotate & Predict' menu
Assembly: The default assembly name now contains variables for the reads and reference sequences so you can set your preferred naming style once instead of on every assembly
Assembly: Fix bugs when just saving 'used reads' without the contigs. The assembly report would say that no reads were mapped and the iterative mapper would only apply a single iteration
Alignment: Fixed crash when trying to align two alignments together
Workflows: Added option for creating branches in workflows
Workflows: More comprehensive documentation for creating and editing workflows. And more examples
Workflows: Added option to filter by document type
Workflows: Primer design and testing can now be configured from workflows
Workflows: Fixed 'Combine with earlier documents' using incorrect data set when referring to an earlier 'save & continue' step.
Annotate from Database: Fixed crash when source sequences have undirected annotations on them
ACE Importer: Fixed a bug where it would crash on some invalid ACE files
General: Fixed hang or crash sometimes when moving, deleting or modifying lots of documents
Primer testing: Fixed it not finding results in some cases on circular sequences with a target region
Primer design: Option profiles no longer overwrite the target and included region when loaded
NCBI BLAST: Fixed a bug where Binning searches would fail to bin all queries in a batch
Geneious Server:
BioPerl no longer installed as part of Geneious Server as Velvet plugin is now self-contained
Single machine install option configures Sun Grid Engine to use Classic spooling instead of BerkeleyDB for better stability
Better error messages on both client and server when login failure is caused by an exception on Geneious Server

New in Geneious Prime 7.0.1 Beta (Sep 24, 2013)

Sequence Search: NCBI BLAST database names in Geneious now reflect those on the NCBI website more closely
Sequence Search: BLAST result folders now remember which column they are sorted by when switching between folders
Sequence Search: Improved progress and results reporting for BLAST searches
Sequence Search: Simplified options for whether to download matching region, extended regions or full sequences.
Sequence Search: Fixed bug causing downloading sequences to get unselected
Sequence Search: Results exported from 7.0 can now be imported into 6.0 and later
Sequence Search: Fixed crash when running on sequences in a shared database
Contig, Alignment and Sequence Viewer: Fixed mouse cursor going invisible or being incorrect sometimes
Contig, Alignment and Sequence Viewer: Fixed annotation text inside annotations sometimes extending outside the annotations
Contig, Alignment and Sequence Viewer: Reverting editing annotations on alignments now keeps the alignment aligned if possible
Contig, Alignment and Sequence Viewer: Improved performance dealing with genomes fragmented into thousands of sequences (for example 10,000 or more sequences, where some sequences in the genome are longer than 100,000bp)
Contig, Alignment and Sequence Viewer: Contig, Alignment and Sequence Viewer: Improved performance and nicer rendering of annotations
Primers: Improved handling of gaps when designing on an alignment
Primers: Fixed crash editing the primer annotation of an oligo sequence
Primers: Improved progress reporting
Workflows: Added sample workflow to reverse complement all selected sequences, sequence lists, or alignments
Workflows: Fixed crash when running some workflows on alignments or chromatograms
Workflows: Added sample custom code workflow to set the truncated status on annotations
Workflows: Improved custom code editor including code completion, context sensitive javadoc and nicer compilation errors
Import/Export: Fixed crash which could occur when exporting unsorted contigs with trimmed regions to BAM+BAI format
Import/Export: Respect RGB values in BED files
Cloning: Gateway Cloning now displays information about the reaction it will perform before proceeding
Cloning: Gibson Assembly will no longer fail if a primer has multiple binding sites, instead a warning will be displayed in the report
Annotation Editing: Fixed some annotation types (e.g. trimmed or overhang) not being recognized after being edited
Extract Annotations: Improved performance
Removed Pfam services and operations
Separate by Barcode: Fixed sequences being incorrectly assigned to barcode groups in some situations when the linker sequence isn't found. This happens when using linker sequences with large numbers of Ts or As near the ends and with high mismatches in the linker.
Preserve annotations on consensus when concatenating alignments
Sequence Search: Fix issue where downloaded full BLAST results did not replace their summaries
Assembly: Fixed hang or poor performance viewing assembly reports which contain links to thousands of contig documents
Variant Finder: Better default settings and improved strand-bias filtering on Illumina paired read data
Fix a crash caused when using generate consensus on documents with inconsistent document fields produced by the Biocode LIMS plugin
Alignment: Better results when using automatically determining direction on free end gap alignments
Annotate From Database: It now will transfer truncated annotations from the source sequences
Transfer Annotations: Similarity slider can be set to 0% to transfer all annotations in alignments regardless of similarity
Fixed situation where floating license would have to be re-activated every time Geneious is started on some Macs

New in Geneious Prime 7.0.0 Beta (Sep 4, 2013)

Copy with Annotations - annotations are now maintained when copying sequences
Gibson Assembly - One-step cloning of fragments using Gibson assembly including automated primer design and batch cloning/shuffling
Codon Optimization - Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.
TOPO Cloning - One-step cloning of fragments into a vector using TOPO
Workflows (Beta) - New interactive tool for creating automated workflows that run any of the existing tools in Geneious
Alignment Features:
Display nucleotide alignment as its protein translation (Option to hide nucleotides in Alignment View)
Added 'Pairwise % Positive' on which indicates the percentage of amino acid pairs that have positive scores in the BLOSUM62 matrix.
Improved quality of 'automatically determine direction' setting
Sort sequences by the number of differences from the reference sequence
Hold down the SHIFT key when inserting to push the alignment sequence left instead of right.
Sequencing and Assembly Features:
Coverage graph: Added visualization of minimum/mean/maximum coverage when zoomed out. Added highlight coverage above threshold option.
Separate by Barcode: Included 454 Rapid MID barcodes, support for trimming barcode specific sequences from the other end, and better handling of primers/linkers containing ambiguities
Fields and notes from contigs are transferred to the consensus when extracted, via sequence viewer extraction, Generate Consensus Sequence operation, and assembly.
Alignment/Contig Viewer: Consensus sequence displays translation using the reference sequence CDS annotations when translation by annotation is on and the consensus sequence has no annotation at that position
Contig Viewer: Improved performance viewing data with high coverage variance (e.g. rnaSeq data)
Consensus: When coverage or quality is below a specified threshold you can choose to call either ?, N, Gap, or the reference sequence value
All newly created contigs will have a mean coverage field in the document table. All newly created reference sequence contigs will have a '% of reference sequence covered' field
Read Mapping: Improved results when mapping to genomes with repetitive regions
Variant Finder: 'Don't find variations in annotation types' and 'Only find variations in annotation types' settings now work on consensus sequence annotations (useful on de novo assemblies)
New Downloadable Plugins:
RAxML - Randomized Axelerated Maximum Likelihood
GARLI - Genetic Algorithm for Rapid Likelihood Inference
FastTree - Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
LastZ - BLAST-like alignment tool for the pairwise alignment of chromosome-sized nucleotide sequences
Bowtie2 - Sequencing read aligner
Velvet - De-novo assembler for very short reads
Dynamic primer editing allows modification of primer annotations and calculates characteristics in real-time as changes are made
Primers are now designed on the consensus of alignments and contigs
Primer Trimming: If you select only one end to trim from, the trimmed region will extend towards that end instead of respecting the direction of the primer.
Primer Trimming: Made the 10,000 sequences limit at which it doesn't annotate trimmed primers user configurable from Preferences->General->Advanced->Trimming.maxSequencesToKeepExtraAnnotations
BP, LR and One Step Gateway operations merged into a single Gateway operation
Custom ladders for Virtual Gel: You can now modify the ladders and add new ones
Enzyme table now has a search box to find enzymes by name
All source properties on Genbank sequences (eg. country, strain) are now available as columns in the document table
The following graphs in the alignment, contig and sequence viewer can be exported to CSV and WIG file formats: Coverage, Identify, Sequence Logo (entropy), GC Content, Hydrophobicity, PI, Protein Coding Prediction, and Amino Acid Charge
Fasta exporter: Added option to exclude sequence descriptions and option to not replace spaces in the name with underscore characters.
Nexus exporter: Added option to replace spaces in the name with underscore characters.
Batch rename: Can now rename fields of aligned sequences (when the sequences are writable)
More special characters are now allowed in Annotation names and Meta-data fields (eg. greek)
Copy Annotations in selected region allows selection of multiple sequences again
Extracting multiple intervals from chromatogram now keeps sequence as chromatogram if any intervals contain chromatogram values. Same with sequence with quality only.
Redesigned Add 5' extension operation that allows adding several extension parts in one step
Added ability to drag and drop URL into Geneious to import the document at that URL
Annotations table: Minimum, Maximum, and Length columns now use less than or greater than symbols for truncated annotations
Sequence searches now appear in the default operation results directory, rather than under the search results service
Reduced memory usage on local databases containing lots of documents
Protein summary documents from NCBI searches are automatically converted to full documents
Sequence Viewer: Uses the "Genetic Code" property on documents and saves changes back to that property rather than using its own preferences. Also allows you to set a default genetic code.
Sequence Viewer: When an annotation is selected, you can press the left then right cursor keys to set the cursor position to the left hand side of the annotation. Or press the right then left cursor keys to set the position to the right hand side.
When extracting annotations of a single interval from a single sequence, it is now possible to concatenate them
Custom Blast: Fields on documents added to the database (e.g. organism) now appear on the results of custom blast searches.
Custom and NCBI Blast: Added option to automatically download full sequences of hits or just the region surrounding the hit.
Sequence Viewer: Right click menu option to 'Copy Name and Bases' is now available on stand-alone sequences
Add/Edit Annotation in sequence viewer allows you to delete custom annotation types from the dropdown
Sequence Viewer: Bases that have been edited are now highlighted in bold
Primer Choosing: Improved performance choosing primers when you have thousands of primers in your database
Sequence Viewer Printing: Added option to turn off shaded annotations when printing
Plugin Development: Added support for 3rd party plugins to provide statistics in the sequence/alignment/contig viewer
Improved Shared Database performance. Indexing of documents is also now done in the background rather than immediately.
Other Notes:
Geneious now bundled with Java 7 on Windows and Linux
Collaboration is no longer bundled with Geneious, it is now a downloadable plugin
Mac OS X 10.5 Leopard is no longer officially supported
Smart Agents/Folders removed from Geneious. Other aspects of agents are unchanged.
"Find Annotations" renamed to "Annotate From Database"
Bugs fixed:
Copying/transferring annotations between sequences in alignments excludes the annotated translation property of source annotations
Sequence Viewer: Fixed 'annotate & predict' results (e.g. trimming) being incorrect if you make changes (e.g. sorting data) while the operation is running
Sequence Viewer: Annotation tooltips wrap long property values to the next line instead of truncating them
Fix issue where the Att site annotator would mistake AttB sites at the end of a linear sequence for AttL sites
Improved recognition and handling of unreliable network file systems when storing your Geneious data on them
Annotation types are now properly case-insensitive, eg. "CDS" is the same as "cds"
Fixed poor performance when viewing some circular contigs containing sequences with large internal gaps
Fixed some cases where setting custom colors of annotations didn't work
Stopped the Mac OS firewall continually prompting about Geneious in many cases - modifying the max memory setting in Geneious will still cause the issue

New in Geneious Prime 6.1.6 (Jun 20, 2013)

New in Geneious Prime 6.1.5 (May 13, 2013)

New in Geneious Prime 6.1.4 (Apr 10, 2013)

New in Geneious Prime 6.1.3 (Mar 27, 2013)

New in Geneious Prime 6.1.2 (Mar 5, 2013)

New in Geneious Prime 6.1.1 (Feb 27, 2013)

New features:
Sequence Viewer: Can revert editing annotations (Insertions, Replacements, Deletions)
Bugs fixed:
Alignment Viewer: Fixed crash when searching for long text on alignments with the 'Allow extra gaps in sequence' setting on
Alignment Viewer: Fixed crash when clicking on annotations in pairwise alignments when the consensus sequence is off
Contig Viewer: Fixed it incorrectly scrolling down when zooming in sometimes
Contig/Alignment Viewer: Fixed hangs when deleting large selections. Also improved deletion behaviour to replace non-gaps with gaps when deleting
Stop crash when starting up when data is stored on an unmounted network drive
Fix issue where queueing for already-queued FlexNet license would stop you from getting the license when it came available
Fix potential hang on shutdown (due to preference clearing issue)
Stop sequences imported from VNTI's .gb format having "(modified)" appended to the name
NCBI BLAST available in restricted version again
Fix crash in feature finder when searching for features annotated on reverse of protein sequence
Improvements to queueing behaviour of FlexNet and Sassafras floating licenses
Nexus importer now importing attributes as document fields
Fix crash in BAM exporter when multiple documents have same name
Fix off-by-one error in Gateway annotator which could lead to crashes in Gateway operations
Clipboard Csv/Tsv import now offers you the choice of which of the two formats to import as. Previously it would erroneously choose the first format which was well-formed.
Fixed a bug where too many excluded regions were being sent to primer3 when primer design was run on some alignments
Made several consistency changes when importing/creating primers that were too short or too long for primer3, across several tools
Fixed a crash in Primer testing when a match on a circular sequence with mismatches fell over the origin
Additional Notes:
BWA updated to 0.6.2 (Geneious Server)
Velvet updated to 1.2.08 and Velvet optimizer updated to 2.2.5 (Geneious Server)

New in Geneious Prime 6.1 (Feb 27, 2013)

Primer Design:
New cloning primer design task added for designing primers with fixed 5' binding positions
Repeat library mispriming added to avoid binding to known repeats
Primer extensions can now be chosen from the primer design options
Designed primers now have nicer names
Sequence View:
When adding or editing annotations you can choose which track they are on.
Replaced the "Move all of annotation type" option with a more general "Edit all of annotation type" option.
Added right click option to copy a sequence name or other displayed field.
Removed restriction on maximum length of text that can be searched for as long as interpreting ambiguities is turned off
Alignment/Contig View:
Added option to hide columns with more than X% gaps
Can drag select the alignment numbering to select all sequences in alignments/contigs
Added find dialog option to allow gaps between characters being searched for
Improved rendering performance (5 times faster in some cases)
Custom BLAST now supports BLAST+ (existing users will have to upgrade blast manually, new users get BLAST+ by default).
Back Translate now has codon usage tables for producing unambiguous nucleotide sequence (uses EMBOSS tool backtranseq)
DNA/RNA fold view now available on two sequences, showing how the two molecules bind to each other (uses Vienna rnacofold 2.0.7)
DNA/RNA fold view updated with new stats panel, better probability color scheme and new energy models
High/Low Coverage Finder: Added option to merge annotations less than a specified number of bases apart.
More things are multi-threaded which makes them faster (e.g. trimming, read mapper indexing)
De Novo Assembly: Slightly better results on gappy data
Lengths Graph: Added option to display contig lengths
New "Grade" column for sequence search results that combines E-value, identity and query coverage in to a single percentage
Cut positions in enzyme table viewer split into count and positions for easier sorting
Lambda PFG, Low range PFG and Lambda DNA-BstEII ladders added to virtual gel view
New geneious.properties file can be used by admins to configure geneious
Text View now available when several documents are selected
New Bowtie2 assembly option added on Geneious Server
Bugs fixed:
Circular contigs now correctly render graphs (e.g. chromatograms) on sequences that wrap past the circular origin
Fixed a crash when importing primers from csv of longer than 36bp
Additional Notes:
Sample documents have been changed significantly
The Solaris operating system is no longer supported officially
Most text is now rendered clearly on Retina display macs
Trial licenses now have to be requested and activated
Vienna rnafold updated to 2.0.7
All EMBOSS tools updated to 6.5.7
Bowtie updated to 0.12.8 (Geneious Server)
SOAP2 updated to 2.21 (Geneious Server)

New in Geneious Prime 6.0.6 (Feb 11, 2013)

New in Geneious Prime 6.0.5 (Dec 12, 2012)

New in Geneious Prime 6.0.4 (Nov 28, 2012)

Sequence Viewer: Fixed hang working with annotation types in tracks that contain '_' or '.' in their type name
Sequence Viewer: Fixed crash in rare situations when clicking on annotations in contigs
Sequence Viewer: Fixed crash and/or loss of newly added annotations on consensus sometimes when saving contigs
Sequence Viewer: Fixed poor performance/hangs viewing large contigs with non-trim annotations on the reads
Sequence Viewer: Fixed statistics that are too small to read sometimes
Reference assembly: Fixed crash and/or incorrect results when choosing to map paired reads to all matching locations.
Reference assembly: Fixed poor sensitivity mapping to genomes of several hundred MB (larger genome sizes (e.g. human genomes) were fine). The increased sensitivity will also slightly improve small genome results.
Reference assembly: Fixed poor sensitivity mapping reads spanning the origin of circular reference sequences
Reference assembly/Find Annotations: Fixed crashes when running out of memory.
Variant Finder: Fixed crash when there is an insertion variant in a repetitive region at the start of the reference sequence
Contigs: Fixed crash when creating contigs with a single reference sequence exceeding 1.8GB
Contigs: Fixed out of memory errors and poor performance when working with lots of contigs
Contigs: Fixed crash when deleting the ends of circular contigs.
Fixed crash when using consensus 'Ignore Gaps' setting combined with 'Assign Quality: Highest'
Fixed crash in MUSCLE alignment when MUSCLE runs out of memory but still returns results
Streamlined selection in 3D Structure viewer
Fixed crashes when downloading Whole Genome Shotgun records from NCBI
Fixed hangs associated with the use of the feature finder
Fixed bug stopping Geneious from being able to change its max memory on Windows sometimes
Fixed hang when extracting multiple large regions from a sequence list or contig
Stopped errors from custom BLAST from being suppressed when the entire BLAST failed
Fixed Gene documents having their dates one month in the future from where they should be
Stopped Vector NTI database import from failing completely when a document's parents unexpectedly have length zero
Fixed multiple dialogs being popped up when queued Sassafras license is checked out but user does not confirm
Stopped NCBI Gene database downloading documents multiple times when there is a connection error with NCBI
Added warning when large NCBI BLAST fails due to being too computationally intensive
Fixed translation in all 6 frames from using frame one only
Stopped stop codon from being included when extracting translation from sequence viewer

New in Geneious Prime 6.0.3 (Nov 7, 2012)

New in Geneious Prime 6.0.2 (Nov 6, 2012)

New in Geneious Prime 6.0.1 Beta (Oct 18, 2012)

New in Geneious Prime 6.0 Beta (Oct 18, 2012)

Primer Design and Testing:
primer3 upgraded to version 2.3.4
Hairpin and dimer characteristics now calculated as melting point (Tm)
Design on sub-region of a long sequence is much faster
Updated melting point calculation parameters
Primer testing performance improved
Selecting two nested regions (by holding ctrl/cmd) in the sequence view will now set the included and target regions
Sequence/Alignment/Contig Viewer:
Reference sequence floats at the top like the consensus sequence
Can choose to number just the alignment without also numbering the reference sequence
Annotations with db_xref links and from dbSNP are now hyperlinked to relevant web site entry
Statistics display the percentage of bases that are at least quality 20, 30 and 40.
Added option to change the thickness of annotations
Nicer positioning of annotation labels
Can edit properties (e.g. description) of sequences in sequence lists and alignments
Improved support for read mapping when choosing to map reads to multiple locations:
Coverage graph and find high/low coverage weight reads less based on the number of locations they map to
Variant finder and consensus sequence generator: Added option to ignore reads mapped to multiple locations
Reference assembler supports using the "map reads to multiple locations" on paired reads
Contig Viewer: Added '# Mapped Locations' color scheme
Contig Viewer: Status bar indicates number of locations the read is mapped to.
Assembler has new option to not map reads at all that would otherwise map to multiple locations
Variants Finder:
Added option to include the sequence names contributing to each variant in the annotation
Added 'Homopolymer quality reduction' setting to assist in eliminating false variants
Amino acid changes reported now take into account variants elsewhere in the codon
Added 'Average Quality' property on annotations
Extended option limiting variations to within annotations of a particular type to also allow finding variations within a specified range of those annotations
Import/Export:
Added VCF import
Added support for publishing figures to SWF and EMF
Added ability to import SAM/BAM file against subsequence of reference
Fastq import can import multiple files with same quality settings
Geneious can now import files that have been zipped or gzipped
Assembly:
De Novo Assembly: Added option to only use percentage of input data for better performance when you have too much data
De Novo Assembly: Improved assembly results
Reference Assembly: New fine tuning algorithm that generates much better results, is faster, and generally uses less memory
Extraction:
Extraction, reverse complement and translate have document history
Fixed issue where extension ended up at wrong end of primer extracted from reverse strand
Added 'Complement Only' and 'Reverse Only' operations (this is not in default distributions - it needs to be installed from the plugins window)
Extract Annotations now lets you choose what other annotations from sequences are included in extraction
New Feature Finder automatically annotates plasmids and other sequences with database of features
Annotations Table in separate tab now supports editing
Sequence/Alignment/Annotations Viewers: Filter box now provides more powerful field-based filtering
Forwards compatibility. Geneious 6 will be able to handle most documents that people export or put in shared databases using future versions.
Circular reference sequence assemblies: Contig viewer displays them correctly and consensus calling, variant finding and high/low coverage finding and statistics correctly handle them
High/Low Coverage Finder: Nicer track names for contigs with reference sequences (like the variant finder has)
Consensus: When the reference sequence has no coverage, you can now choose to call either ?, N, Gap, or the reference sequence value
Find Duplicates operation gives option to create new sequence list containing duplicates
Modified date field is no longer updated on documents used as input to operations
GenBank "contig" download downloads the full document and not the documents that comprise it
Sequence Search: Now automatically ignores leading and trailing trim regions
Full screen now supported on Mac OS X Lion and above
Improvements to transcription factor search output: Transcription factor name, clickable link out to Tranfac entry, explanation of quality values.
New "Info" view tab which contains Lineage, History and Properties. Properties combines the previous "Notes" view with the ability to edit common fields like Description and Organism
Shared Database: Folders that a user cannot view are now hidden by default. They can be shown again by right clicking on the root database folder.
Tree viewer now shows consensus support just above nodes
Profile Alignment plugin turned off by default
Collaboration menu moved under Tools menu
Lots of other little improvements
Bugs fixed:
Sequence Viewer: When zoomed out, adjacent annotations looked like they were overlapping
Editing 'Topology' field directly instead of changing it via the Sequence menu didn't work
Additional Notes:
Geneious is signed on Windows and MacOS. This means it can be downloaded from Internet Explorer 9+ without warning and Gatekeeper will not reject it.
Geneious now requires Java 6. Geneious will no longer run on Java 5. This means Geneious will no longer run on platforms where Java 6 is unavailable such as Power PC Macs and Mac OS X 10.4 (Tiger)
Geneious is now only available in one package for Mac OS X. This runs in 64 bit mode by default, but can be changed to run in 32 bit mode.
Server Databases has been renamed to Shared Databases to avoid confusion with Geneious Server
Geneious now collects anonymous usage information (with your permission) to help us make improvements
Changes to licensing:
Geneious Pro/Basic terminology removed
Must now enter a license or start trial when starting Geneious for the first time
Geneious Pro days no longer occur

New in Geneious Prime 5.6.6 (Oct 15, 2012)

New in Geneious Prime 5.6.5 (Jul 26, 2012)

New in Geneious Prime 5.6.4 (Jun 13, 2012)

New in Geneious Prime 5.6.3 (May 14, 2012)

New in Geneious Prime 5.6.2 (Apr 23, 2012)

New in Geneious Prime 5.6.1 Beta (Apr 11, 2012)

New in Geneious Prime 5.6 Beta (Mar 27, 2012)

Parent-Descendant tracking:
Sequences can be actively linked to each other as parent/descendants. Active links are created by all cloning related operations.
When a parent sequence is edited, Geneious can propagate the changes to all actively linked child sequences, save the changes to a copy or deactivate the links.Pro-only
Documents can also be inactively linked to each other which means there is a record of their relationship but changes cannot be propagated. All non-cloning operations create inactive links.
New lineage view shows parent and descendant relationships, including active and inactive links and the operations that where performed.
Sequence View Improvements:
Added 'By Direction' color scheme for coloring sequencing reads based on their direction
Statistics show mean forward/reverse coverage of the selected region Pro-only
Improved performance when viewing contigs with regions of very high coverage (e.g. 5,000+)
Separated "Find in annotations" and "Find in Sequence Names" options to allow efficient annotation searching on big contigs
Improved performance viewing big contigs with annotated reference sequences
Can edit the color of individual annotations Pro-only
Translation now displays both amino acids for ambiguous codons that translate to 2 possible amino acids
Go to base now uses the un-gapped position for the reference sequence in assemblies
New annotation table:
Allows bulk selection, deleting and editing of annotations Pro-only
Improved performance on large data sets Pro-only
Remembers column state between documents Pro-only
Integrated with sequence view so it shares all the same controls Pro-only
Variation/SNP Finder Improvements:
Added 'Minimum Strand-Bias P-value' setting for reducing false SNPs due to sequencing error Pro-only
Better identification of tandem repeat amplification/reduction Pro-only
Track names added to the reference sequence now include the sample name in the track name Pro-only
Added "CDS Codon Number" field to indicate which codon in the CDS the SNP applies to Pro-only
Added "CDS Position Within Codon" field to indicate which position within a codon (1, 2, or 3) in the CDS the SNP applies to Pro-only
Other New Features:
New Align/Assemble menu replaces the separate Alignment and Assembly buttons to make it easy to choose the correct algorithm
De Novo Assembly: Reduced memory usage, improved performance and more accurate memory usage estimates
Improved performance importing fasta/fastq/sam/bam files
Files that are copied from the desktop can now be pasted in to the document table or imported using Import - From Clipboard in the File menu.
Primer Trimming: Improved performance (about 7 times faster) Pro-only
Primer characteristics can now be used for reverse primers and primer pairs Pro-only
Test with Saved Primers now records mismatch locations as annotations and in a new qualifier Pro-only
Extract button added to Sequence Lengths Graph Pro-only
Strip alignment columns can now strip columns containing a certain percentage of gaps Pro-only
Enzymes view is now available when more than one sequence is selected Pro-only
2D DNA fold viwer added which is available on any nucleotide sequence under 3000bp in length Pro-only
Distances view now has # Differences and # Identities matrices Pro-only
Plugin Development/Public API: Improved documentation
When generating consensus trees, they can now be saved to a separate document.
Can sort documents by their color (new color column added)
Bugs fixed:
Reduced memory usage on long-lived databases by storing preferences more efficiently

New in Geneious Prime 5.5.7 (Mar 12, 2012)

New in Geneious Prime 5.5.6 (Dec 5, 2011)

New in Geneious Prime 5.5.5 (Nov 21, 2011)

New in Geneious Prime 5.5.4 (Nov 7, 2011)

Bugs fixed:
Sequence Search: Fixed crash sometimes when doing a sequence search
Sequence Viewer: Fixed crash after deleting sequences in genome lists
Sequence Viewer: Fixed hang/crash when resizing some trim annotations
Sequence Viewer: Fixed crash clicking 'go to next annotation' button on some restriction site annotations
Sequence/Contig Viewer: Fixed crash if you delete a track, create one with the same name, and click save
Sequence/Contig Viewer: Fixed crash when loading a document that previously had an annotation selected in a track, but that track was turned off while viewing another document
Alignment/Contig Viewer: Fixed not rendering SNP/coverage annotations on the reference sequence that lie past the ends of the reference sequence
Alignment/Contig Viewer: Fixed it saying you need to zoom in to view reads on contigs that only have a few reads
Alignment/Contig Viewer: Fixed occasional crash when dragging bases/gaps around during alignment editing
Alignment/Contig Viewer: Fixed out of memory crash sometimes when saving new tracks
Alignment/Contig Viewer: Fixed crash sometimes when removing chromatogram sequences from a contig
Assembly: Fixed crash in some cases when mapping a contig to a circular reference sequence. And improved results so that contigs spanning the origin map individual reads to both sides of the origin
SNP Finder: Fixed crash on some data sets.
SNP Finder: Fixed it incorrectly reporting 'no protein effect' when there is a deletion or insertion that doesn't change the amino acid at that point
SNP Finder: Fixed it not reporting results correctly when there are overlapping CDS annotations
SNP Finder: Fixed it not reporting results when choosing to find in CDS annotations only with 'analyze effects on translation' off
SNP Finder: Fixed p-value missing from results in some cases when using exact p-value calculations
Set Paired Reads: Fixed crash when pairing multiple sequence lists by linker.
Set Paired Reads: Fixed crash when repairing reads with mixed relative orientations.
Annotations table: Fixed very slow sorting
Annotations table: Fixed occasional crash when no longer viewed
Primer Design: Fixed a bug where sequences designated as probes were showing up with a forward primer annotation instead
Primer Design: Fixed a bug where the salt concentration was not being taken into account when calculating TM of primers
Primer Design: Fixed a bug where calculating characteristics was failing on multiple selections
Fixed crash sometimes when deleting a folder
Search index: Fixed crash sometimes when building search index for contigs with tracks
Made changes to NCBI BLAST to adhere closer to the guidelines given by NCBI. Geneious will not hit NCBI limits as easily. Also removed the 11kbp sequence length constraint from BLAST searching.
Ace exporter: fixed a bug where it was exporting gap qualities
Fixed major crash under Java 7
Fixed issue where Geneious reports incorrect codon_start on CDSs on documents downloaded from NCBI which have foreign intervals

New in Geneious Prime 5.5.3 (Oct 10, 2011)

Bugs fixed:
Assembly: Fixed crash sometimes when generating assembly report
Assembly: Fixed crash sometimes when assembling gappy reads to a circular reference sequence
Assembly: Fixed 'Map multiple best matches' mapping reads with gaps to the same location multiple times
Alignment/Contig Viewer: Fixed 'Hide gaps in reference sequence' discarding annotations covering gapped regions in the reference sequence
Alignment/Contig Viewer: Fixed crash when saving changes made to some alignments
Contig Viewer: Fixed changes getting lost in some situations when saving after editing the reference sequence in a big contig
Contig Viewer: Fixed hang sometimes when selecting on big contig documents
Sequence Viewer: fixed crash pressing ctrl-alt-g (go to residue) after selecting a document but before the sequence viewer has finished loading
Sequence Viewer: Fixed crash sometimes if there isn't enough memory to load a big track on a sequence
Sequence Viewer: Fixed annotations in tracks getting drawn on top of other sequences in some situations
Sequence Viewer: Fixed crash when editing some trimmed sequences
Sequence Viewer: Fixed very slow initialization on sequence lists containing thousands of sequences with tracks on each sequence
Sequence Viewer: Fixed undo not working correctly when dealing with some types of changes to tracks
Sequence Viewer: Enabled genome viewer chromosome selector (available when at least one sequence has 100,000 or more bases) on sequence lists with more than 1000 sequences
Local Database: Fixed failure to save documents sometimes
SNP finder: Running on multiple contigs at once that referenced the same reference sequence would generate identically named tracks and only the first one would get displayed
Sequence viewer: Fix bad performamce extracting millions of reads from a sequence list
Sequence viewer: Fix crash extracting sub-alignment containing sequences of all gaps and the consensus
Fixed tracks not getting saved sometimes when saving them on contigs/alignments
Fixed a few crashes in the SAM/BAM importer

New in Geneious Prime 5.5.2 (Sep 27, 2011)

New in Geneious Prime 5.5.1 Beta (Sep 20, 2011)

New features:
Annotations table: Added new columns with the minimum and maximum values in original sequence coordinatesPro-only
BLAST query and hit sequences have description Pro-only
Bugs fixed:
Fixed a bug where Batch Rename would fail to rename large sequence lists.
Greatly improved speed of back up operation when doing full archive backup (no longer uses compression)
Fixed custom fields being lost when exporting documents in Geneious format and importing them on another machine
Fixed so that if you unselect the document while an 'annotate & predict' operation is running you can still get the results
Fixed some fields not getting indexed for searching on big documents
Fixed out of memory errors when indexing big documents
Improved memory efficiency of BED importer so you can import a densely annotated genome (eg SNP files from UCSC) in a small amount of RAM
Fixed bug where Jmol viewer did not restore state first time showing molecule after save
Fixed crash in ACE importer when bases are invalid
Fixed GenBank importer not offering to create sequence list
Fixed bug where Geneious thought you could run annotation generators on unaligned sequences when the sequence viewer wasn't loaded
Fixed assembly crash when assembling existing contigs containing trim annotations covering gapped regions
Annotations table: annotations that start or end at the origin of a circular sequence now show min/max values of the sequence length rather than 0Pro-only
Annotations table: now displays annotations from consensus sequence tracksPro-only
Annotations table: now remembers widths of resized columnsPro-only
Annotations table: sorts decimal and scientific format numbers correctlyPro-only
Fixed issue where the extraction of an annotation with overlapping intervals would end up with extra intervals
Made fasta and fastq importer replace preformance-killing names with better ones
Bug fixes in Sequence/Contig Viewer:
Fixed crashes and hangs caused when trying to view too many tracks to fit in memory
Fixed tracks crashing or behaving wrongly after reordering sequences
Fixed track names being rendered too close or overlapping with the sequence name
Fixed crash when viewing sequence lists containing tracks after some sequences have been deleted from the list
Fixed crash when saving some contigs after seeing a conflicting changes message
Fixed 'Annotations are arranged more efficiently on genomes' not working on circular genomes
Changed units in sequence viewer from Mb to Mbp
Fixed annotations in tracks on consensus sequence appearing in the wrong location when 'hide gaps in reference sequence' is on
Bug fixes/improvements in UCSC annotation track downloads Pro-only:
Warning if chromosomes are wrong length
Nice names for genomes
Better sorting for genomes/chromosomes
File size does not stop displaying when you change chromosomes
Stop displaying tracks that cannot be accessed by HTTP
Fix issue where annotations could appear on the wrong chromosomes
Allow annotation of sequences regardless of what documents they're grouped into (eg 1 standalone sequence and 2 sequence lists)
Fixed horrible performance when running UCSC again without having saved the changes produced from an earlier run
Bug fixes/improvements in extraction/reverse complementing/translating in sequence viewer Pro-only:
Changed behaviour of extraction of whole sequences from alignment to create new sequences rather than going to existing references
Fixed crash when extracting annotation with two identical intervals on same sequence
Made options remember preferences on appending "extraction" to names, extracting to alignment vs sequence, extracting selected vs entire sequences
If you extract a whole circular sequence from an alignment the result is now circular
Bug fixes/improvements in SAM/BAM im/exporter:
Fixed issue finding reference sequences when importing SAM/BAM files with no header
Fixed crash when exporting sequence with unreasonably high quality to SAM/BAM format
Fixed crash importing with a reference with quality that has gaps introduced
Fixed behaviour when importing or exporting contigs where one or more reads start after the end of the reference
Fixed crash when file consists entirely of pairs without their mate

New in Geneious Prime 5.5.0 Beta (Aug 30, 2011)

Sequence View Improvements:
New annotation track functionality that groups annotations from a common source so they can be rearranged, colored, shown/hidden, deleted etc Pro-only
Added an interactive mini-map that shows your current position in the genome and a summary of annotations
Added a real-time annotation filter in the annotation controls Pro-only
Added a chromosome selector when viewing an entire genome as a sequence list (saves memory and improves performance)
Added a slider for changing the zoom level on genomes
Redesigned "go to position" to have a single input field and a shortcut button in zoom controls on genomes
Annotations are arranged more efficiently on genomes
Positions in big sequences are now rendered like 45.2 mb instead of 45,200,000
Added ability to extract multiple primer annotations simultaneously
Annotation generators can now run on more than one alignment simultaneously. Eg. "Find Variants/SNPs" Pro-only
"Add Annotation" button can now create separate annotations for each selected region Pro-only
Coverage graph: Added logarithmic scale option and added mean coverage indicator on scale bar.
Can click on annotation types in the controls to change all annotations of that type to a new type Pro-only
Added "Copy (reverse complement)" to right-click popup menu
Other new features:
New One Step gateway operation that does BP and LR reactions in one step Pro-only
New Download Annotation Tracks operation to annotate genomes with data from Broad Institute Pro-only
New CSV/TSV Importer:
Import primers, probes and nucleotide/amino-acid sequences from spreadsheets
All operations can now have their setting saved to a profile for re-using later or sharing with other people Pro-only
New Support button that makes it easier to contact our support team and attaches system information so we can answer you more efficiently
New 'Compare Annotations' operation to compare annotations of different types on a sequence Pro-only
Primer Testing: Can now test a selection of primers from your database Pro-only
New graph view displaying distribution of paired read distances in a contig Pro-only
Distances viewer now works on alignments and can display a percent identity matrix (plus other small improvements) Pro-only
Share Geneious documents and visualizations with your friends and colleagues via Email, Twitter or Facebook
New TSV (Tab separated values) exporter
Import sequences by pasting straight in to Geneious
New checkbox column in table makes it easier to select multiple documents (no key presses required)
SAM/BAM importer
Improved performance and progress reporting
Groups unmapped sequences by reference when known
Can import more than one SAM/BAM file at once
Find Variations/SNPs improvements Pro-only
Added option to specify what properties of CDS annotations to copy to SNP annotations. Added CDS interval number property to SNP annotations
Added p-value to variations and added a maximum p-value threshold for finding variations. This fixes incorrect variations reported around 454 homopolymer regions
Added option to find variations within the sample (rather than comparing to the reference sequence)
Ambiguities characters are now interpreted instead of being treated as different character types
Assembly improvements Pro-only
Better results when assembling to large reference genomes
Added setting to save used reads (and optionally their non-mapping mates)
Increased maximum reference sequences from 10,000 to 25,000 and added Preferences->General->Advanced->Assembly.maxReferenceSequences to increase it further (although this is not recommended as performance will be poor)
Added 'Map multiple best matches' setting (for unpaired reads only) to read mapping/reference sequence assembly
Added 'Assemble each sequence list separately' setting for performing multiple assemblies in one step
CSV export can now include complete sequence
Chromatograph View: Highlights the selected region from the sequence view
GFF importer imports GTF format
GFF importer more memory-efficient
Strip alignment columns: can now strip every third position or columns containing one or more gaps Pro-only
Transfer annotations: Added option to transfer annotations to the consensus sequence Pro-only
Annotations table: Minimum, Maximum and Length columns values no longer include gaps in calculation. Added new columns with the old values Pro-only
Annotations table: Added horizontal scrollbar and auto-size width of columns Pro-only
Annotations table: Enhanced performance and fixed hangs when sorting or filtering extremely large numbers of annotations Pro-only
Set Paired Reads: Added option to pair reads by name and now handles missing reads Pro-only
Concatenation can now add NNNNN spacers between sequences Pro-only
New column on contigs and alignments that displays the reference sequence name
GenBank Flat importer now copes if there's no locus
Now possible to import CAF file(s) and other file(s) simultaneously
FASTA exporter can limit lines to 80 characters
ClustalW is now bundled with Geneious Pro-only
Added ability to release floating license Pro-only
Bugs fixed:
Fixed partial CDS annotations (which include only a subset of the full CDS intervals) displaying out of frame annotations when extracted from a document containing the complete CDS
Fixed deletion annotation at end of sequence not being displayed in sequence viewer
Batch rename now offers Description of the sequences in an alignment as a readable field when renaming
Primer characteristic calculation including during oligo import from VectorNTI much faster
Fixed crashes when alignment engines like MUSCLE and ClustalW return no alignment or unexpectedly return a local alignment
Reduced memory usage required to move large documents from one folder to another
Sequence similarity statistics respect trim annotations better
Improved speed of FASTA im/exporter
Improved speed of Find Duplicates
Decreases memory usage of "Extract sequences from list"
Avoided hang when adding custom BLAST database which produces lots of errors from formatdb
Stopped GenBank exporter adding name label to features in unmodified documents
Fixed crash when extracting contig from contig and some sequences in the extract region consist entirely of gaps
Made Gateway Cloning cope with sites over origin when sites are attX1 and attX2; better error message for multi-site
Stopped dialog popping up repeatedly if support on your permanent license expires while Geneious is not running
Geneious now deletes file results from cancelled backup
Fixed crash in RNAFold when output in unexpected format
Fixed crash in SAM importer when file contains unaligned records without base sequence
Fixed crash in SAM importer when encountering the X operator
Fixed crash in download from NCBI when mandatory element missing
Stopped ClustalW importer potentially importer alignments with mixture of nucleotide and protein sequences
Stopped Custom BLAST losing document fields such as organism
Stopped VNTI import crash when different molecules have custom fields with different fields
Improved performance when editing bases in a genome
Stopped Geneious assembler falsely identify regions in large genome as repetitive (and not mapping reads there)

New in Geneious Prime 5.4.6 (Jul 25, 2011)

New in Geneious Prime 5.4.5 (Jun 30, 2011)

New in Geneious Prime 5.4.3 (Jun 7, 2011)

New in Geneious Prime 5.4.3 (May 12, 2011)

New in Geneious Prime 5.4.2 (Apr 26, 2011)

New in Geneious Prime 5.4.0 Beta (Apr 1, 2011)

New features added in Pro version only:
Support for Multi-site gateway cloning
BAM format import and export (including BAM index file)
BED format import and export
SAM format export
Set the color of folders and documents in local and server databases
RNA Fold viewer scrolls to selection
Better results when reference sequence assembling.
Codon usage statistics added to the Statistics tab in the Sequence and Alignment view
The direction of sequencing reads can be set before the assembly process using "Set Read Direction" in the Sequence menu
Improved performance and greatly reduced memory usage when dealing with large numbers of sequences (both stand-alone and in contigs)
BLAST searches now have the option to return a query-centric alignment document only
BLAST searches now have the option to bin queries into those with hits and those with none, without the need to download entire hits (faster than a standard search)
New features:
Added "Whole Words Only" checkbox to local documents searching so that you can search for partial words
Added "Find All" button when using "Find in Document" on the sequence/alignment viewer
Can select multiple folders for moving/deleting and for showing the contents of them all at once
Bugs fixed:
When a sequence is circularized, annotation intervals extending past the ends of the sequence are now truncated
When a sequence is de-circularized, annotation intervals spanning the origin are split into multiple intervals
Fixed poor performance when viewing some sequences with over 100,000 annotations
Empty sub-folders are now kept when exporting folders
Separate by barcode works on already paired reads and lets you choose which sequence in the pair has the barcode
Fixed problem with garbled fonts on some systems
Fixed de novo assembler running out of file handles on machines with lots of processors
Greatly improved the speed at which Geneious performs large batch BLAST searches
Fixed crash when loading some contigs (which would also cause search index to crash)

New in Geneious Prime 5.3.6 (Mar 30, 2011)

New in Geneious Prime 5.3.5 (Mar 3, 2011)

New in Geneious Prime 5.3.4 (Dec 21, 2010)

New in Geneious Prime 5.3.3 (Dec 13, 2010)

New in Geneious Prime 5.3.2 Beta (Dec 8, 2010)

New in Geneious Prime 5.3.1 Beta (Nov 29, 2010)

New in Geneious Prime 5.3.0 Beta (Nov 15, 2010)

Next-Gen Sequencing:
Can split unprocessed 454 paired reads apart based on the presence of a linker in the middle of a sequence using 'Set Paired Reads' from the Sequence menu
Can split multiplexing data (e.g. 454 MID sequences) using 'Separate Reads by Barcode' from the Sequence menu
Can split Polonator paired reads in half from using 'Set Paired Reads' from the Sequence menu
The Geneious reference sequence assembler fine tuning option can be applied to existing contigs without needing to reassemble them
BLAST:
Custom BLAST databases created from sequences in Geneious will now store annotations and return fully annotated hits
If Maximum Hits is set to 1 in Sequence Search, all results are downloaded to a single folder instead of creating many sub-folders
Custom BLAST can now use multiple CPU cores (advanced option added)
Blast hits now have a column in the document table listing the percentage of the query sequence covered by the hit
Can view query centric alignments vertically compressed (like the 'Vertically Compress Contig' setting in previous versions)
Full support for importing GFF 3 format annotations and better options for choosing which sequence(s) to annotate
Trees can now be printed across multiple pages
ACE format exporter for assemblies
GC graph now has "frame plot" option to show GC content in each codon position
Can resize chromatogram traces by dragging them up/down in the Sequence and Alignment Views
Individual chromatogram traces (A,C,G and T) can be hidden in the Sequence and Alignment Views
When viewing vertically compressed contigs/alignments, it shows sequence names even when zoomed out if there is only 1 sequence in the row within the visible region
In an alignment view if you set a reference sequence then the statistics list the percentage of the reference sequence covered by other sequences in the alignment
Tree view allows setting of a maximum length for tip labels, truncating longer labels
Binning parameters can be set for individual folders or documents by turning on "Enable per folder/document binning" in the binning preferences
Primer trimming now has a "Minimum Match Length" option, allowing better trimming of partial primers binding sites
Go to next/previous disagreement button now skips over the middle of contiguous disagreements
Sequence Searches now show up in Operations Table
Whole Genome Shotgun sequences from NCBI can be imported and downloaded
When assembler saves unused reads it puts unused paired reads in a separate list from unused unpaired reads
SNP/Variation finder: Added option to not find variations in regions covered by particular annotation types
New features:
Reduced memory usage when importing big sequences, contigs, and alignments
Bugs fixed:
Editing the consensus sequence in a contig/alignment doesn't modify the reference sequence now
Fixed assembly sometimes introducing excessive gaps around regions that don't closely align
Fixed Maq importer setting incorrect paired read expected distance on some contigs
Numerous small bug fixes in Operations Table
Fixed incorrect concatention of mixed quality and non-quality alignments
Ace importer brings in sections of reads which fall outside the consensus
Trim By primers matches primers partially off the end of a sequence
Fixed base numbering on blasts that find hits on the reverse complement
Fixed unresponsiveness when loading long sequences with many restriction sites into viewers
Fixed bug introduced into multi-user chat in Geneious 5.1

New in Geneious Prime 5.1.7 (Nov 3, 2010)

New in Geneious Prime 5.1.4 (Sep 30, 2010)

New in Geneious Prime 5.1.3 (Sep 21, 2010)

New in Geneious Prime 5.1.2 (Sep 15, 2010)

New in Geneious Prime 5.1.1 (Sep 3, 2010)

New in Geneious Prime 5.1.0 (Aug 16, 2010)

New features added in Pro version only:
Primer browser - Used for choosing primers for testing and trimming. Allows sorting of primers and grouping them in to folders.
New batch rename with complex replacements and the ability to rename any field
realign part of an alignment
Virtual gel viewer now has labels above columns
Extract PCR can now extract all PCR products or the product from any two selected primers
GC content graph
Fragment viewer and digest operation can now digest by each enzyme separately
Assembler now uses multiple CPU cores for improved performance on multi-core machines
Ligate Sequences can now be used to ligate a single linear sequence into a circular sequence
Quality of bases in the consensus can now be calculated as a sum rather than max (more correct)
Vector NTI gel archive importer (.ga4)
Sequence view color schemes can now be completely customized
Document history is now added for assemblies and sequence searches
Can now add a sequence to an alignment without actually performing an alignment
Automatic transfer of annotations to a reference sequence from BLAST hits or aligned sequences
Can manually transfer annotations in query centric BLAST results to the reference sequence
Can add annotations to sequences in 3D structure documents without needing to create a copy of the sequence
Assembler now has a Stop button to get results before assembly finishes
RNA Fold viewer now highlights selections made in other viewers
Assembler now has Minimum Overlap and Minimum Overlap Identity options
New distance matrix viewer for trees - includes display of patristic distances and matrix export
Extract annotations has option to extract entire sequence when it contains a matching annotation
High/Low coverage finder now has an option to only annotate coverage in genes/CDS regions and average the coverage over the gene.
Find variations/SNPs can now be run on the selected region only
Digest Sequences now allows cutting at arbitrary selected positions
Sequence view statistics panel now shows rough DNA melting point
Annotations can now be modified by dragging the ends of them in the Sequence View
Non-highlighted characters in an alignment can now be displayed as dots instead of fading their color
Improved performance and reduced memory usage in both de novo and reference sequence assemblers
Can assemble to multiple reference sequences
Can save/generate consensus sequences directly from assembly instead of or in addition to conitgs
SNP finder records the position of the SNP relative to the start of the CDS annotation it is in
New assembler can now add sequences to an assembly and assemble sequences together
New features:
"Operations" table shows the status of all currently running tasks and a history of recently run tasks.
Back Up button added to the toolbar with a greatly improved back up process
Can now copy text out of annotation information popups in the Sequence View as well as click web links
Ctrl+clicking (Mac OS: Command+clicking) on annotations allows selecting of multiple regions in Sequence View
Nexus exporter has option to export simple form with no meta data (required by some other programs)
The search index can now be paused by clicking on the indexing status on the bottom left
Bugs fixed:
Several improvements to avoid path length limits on Windows systems
Identity graph and other statistics now correctly ignore trimmed regions

New in Geneious Prime 5.0.4 (Jul 15, 2010)

New in Geneious Prime 5.0.3 (Jun 8, 2010)

New features:
Can have the pipe character "|" displayed for identities in the text view for pairwise alignments and blast hits (Advanced options in General Preferences)
Bugs fixed:
Fixed crash sometimes after saving changes to a contig or alignment
Fixed sequence/contig/alignment viewer displaying the original name instead of the current name for some sequences.
Some icons were missing when running Geneious using Java 5
Generating a consensus sequence from a contig ignored the 'Assign Quality' setting if the reference sequence had no quality
Fixed crash during de novo assembly of sequences containing too many ambiguities
Fixed a bug in the generation of assembly reports when assembly from existing contigs
Sequences with quality but no chromatogram trace no longer have the chromatogram icon (eg. extracted consensus sequences)
Fixed crash when concatenating or ligating some types of sequence list documents.
Fixed sequence viewer not displaying some graphs (e.g. CpG Islands) because it wrongly thought the sequence had been edited
Extracting a sequence can no longer result in partial restriction sites or primer binding sites
Fixed annotations appearing 1 off from their correct location when extracting a region from an alignment starting with a gap
Fixed a bug that caused to appear in the export of BLAST alignments in traditional BLAST text format
Fixed crash aligning a sequence consisting entirely of gaps
Improved memory efficiency, progress reporting and cancellability of the SAM importer
Fixed GenBank importer to recognise recognition sequences on enzyme annotations exported from Geneious
Fixed crash concatenating sequences containing quality but no traces
Insert into Vector recognises cut sites that have amibiguities or have direction when they shouldn't
Better error reporting for FLEXnet licenses including trials
Vector NTI importer ignores files starting with ._
Fixed local documents reindexing your entire database sometimes when you restart Geneious before it finishes indexing
Extract PCR Product now works on sequences where primer annotations are right on the end.
Fixed the alignment of text in the blast text view on certain systems

New in Geneious Prime 5.0.1 Beta (Apr 29, 2010)

New in Geneious Prime 5.0.0 Beta (Apr 19, 2010)

New features added in Pro version only:
Paired end read support - For sequence assembly and contig viewer
Improved performance and greatly reduced memory usage on big contigs - Can view contigs of 10 million short sequences in 1GB of memory
Split view - Open documents in multiple views and zoom levels
Deleted items folder - Restore deleted documents (like Recycle Bin or Trash)
Document history - Changes to documents are now recorded for later reference
SNP/Variation finder for contigs and alignments
Assembly maximum mismatches and maximum gaps settings are now percentages proportional to the sequence or overlap length instead of absolute values
Virtual gel viewer
RNA and Primer secondary structure prediction and visualization (uses RNAfold)
Import and view gel image files
MAQ alignment format importer
CAF assembly format importer
SAM format importer
FastQ format exporter
Qual format exporter
Can sort sequences in an alignment by the bases or residues at a particular position
Option to specify the minimum confidence (ie. quality) for a call to be made in the consensus sequence
When a consensus sequence is extracted or generated it will retain calculated quality scores
High/Low Coverage finder for contigs and alignments
Non-cutting enzymes are now added to the "Restriction Sites" table when "Find Restriction Sites" is used
Added server database administration interface
Export images to EPS format
Basic microsatellite data support (includes .fsa format import and viewer)
View settings in the sequence view can be saved as preset profiles
Dotplot now synchronizes its selection with the sequence view
Keyword filtering in the "Annotations" table view
Can now add annotations to the consensus sequence in an alignment
Find in translation for nucleotide sequences in the Sequence View
Find duplicates can now find duplicates in alignments and sequence lists
Batch rename now works on alignment and sequence lists
Concatenate now works on sequence lists
New features:
Can now re-root rooted trees in Tree View
View preferences can now be stored separately for each document in the sequence view
New controls layout in the sequence view
Fragment length is shown when one restriction site is selected and the mouse is moved over another in the sequence view
Added buttons and shortcut keys to the sequence viewer to go to the next/previous annotation of the same type

New in Geneious Prime 4.8.5 (Mar 4, 2010)

New in Geneious Prime 4.8.4 (Feb 10, 2010)

New in Geneious Prime 4.8.3 (Dec 17, 2009)

New in Geneious Prime 4.8.2 (Nov 30, 2009)

New in Geneious Prime 4.8.1 (Nov 25, 2009)

New in Geneious Prime 4.8.0 (Oct 29, 2009)

New features added in Pro version only:
Fast de novo assembly - Capable of assembling 100,000 454 reads or 500,000 Illumina Solexa reads without a reference sequence in a few minutes on a desktop machine.
New dotplot - capable of dotplotting genome sized sequences with brand-new controls (utilizes EMBOSS)
Better handling of next-gen sized data - greatly improved speed and memory efficiency when dealing with large next-gen data sets
Primer extension support - add a restriction site or other extension to primers and Geneious takes this in to account when testing the primer and using it for other analysis
Trim by primers - screen for primers from the local database
Batch export - export several documents to separate files in one step (File > Export > Batch Export)
Color sequences according to their annotations ("By Annotation" option under Colors in the Sequence View)
More powerful primer design on alignments and support for designing primers on assemblies
FastQ file format import
CsFasta file format import
Qual file format import
Add and Remove enzymes from enzyme sets and combine enzyme sets
Search for individual primers from your database that match a sequence
Option to find residues in the translation of DNA (Edit > Find in Document)
Quality measures for chromatograms added to sequence view statistics (Confidence and Expected Errors)
Extinction coefficient for proteins added to sequence view statistics
Read length and coverage statistics for sequencing data added to sequence view statistics
Sort sequences by name and other attributes in sequence lists, alignments and assemblies (right click in Sequence View and under Properties options)
The EMBOSS tools plugin is now included with Geneious as standard (adds many functions)
All models in a 3D structure can now be shown simultaneously in the 3D structure view
Folders can now be copied between server and local database by drag and drop
New features:
Pan in Sequence View by holding Ctrl+Alt while dragging (Command+Alt on Mac OS)
Greatly improved local database start up time for users with large numbers of documents (takes effect after first start up of 4.8)
Geneious export no longer offers compressed/uncompressed format, Geneious format is always compressed with .geneious extension
Sequence view statistics can now be copied to the clipboard
Improved display of multi-interval annotations and primers in the sequence view
Bugs fixed:
Change residue numbering now works on circular sequences
Notes can now be stored in the Server database