SnapGene Changelog

What's new in SnapGene 7.0.3

Oct 11, 2023

Fixes:
Fixed a bug that could trigger a blue screen of death on Windows when monitoring for added, removed, renamed, or moved files in an open project.
Fixed a hang that could occur when editing a primer sequence
Fixed a hang that could occur when setting the numerical origin of a circular DNA sequence if it contained one or more highlighted enzymes.
Fixed a crash that could occur when closing a document before searching a file is complete.
Improved performance and addressed issues when open a project that resides on a cloud backed drive such as Google Drive, Dropbox, etc.
Fixed a bug where clicking the X button in the dialog that pops up asking if you want to save or discard unsaved changes resulted in discarding the changes. Manually closing this dialog now cancels out of closing the document.
Convert U's to T's when converting newly created or imported RNA sequences to DNA
Upgraded Qt to version 6.2.10 in part to include WebP patch

New in SnapGene 7.0.2 (Jul 27, 2023)

Enhancements:
Reduced the size of icons in the top toolbar by default
Improved look and feel of tabs in search dialog
Improved find dialog drop shadow
Fixes:
Fixed a bug that resulted in files and folders that with non-latin characters sometimes appearing not writable when in fact they are.
Fixed a bug where dragging out a selection in map view would stop working after passing over an annotation
Fixed issues with adjusting segment ranges for split features
Fixed selecting mirror files created by previously importing a Vector NTI database
Fixed opening some SeqBuilder files
Fixed importing Geneious files that contain a mixture of sequence types
Fixed a crash that could occur when changing the sequence typology in the New File dialog
Fixed a crash when opening some non-native (e.g. GenBank) files
Improve stability when working with collections
Improved stability when popping a stand-alone window back into a tab
Various other stability fixes
Fixed a bug that resulted in the undo, redo, cut, copy and paste menu actions incorrectly being disabled when using the New File dialog
Fixed an issue that sometimes prevented switching tabs using keyboard shortcuts
Fixed detecting if restriction sites at the numerical origin is methylation sensitive
Fixed displaying quality data in FASTQ files
Fixed a bug where residues in ssRNA secondary structures were not numbered consistent with the sequence numbering
Editing search query no longer triggers a new search unless the change leads to a logical change to the search query
Improved layout and scrolling of content in the search dialog
Support top toolbar menu actions for all file types
Restore the visible state (shown or hidden) of the top toolbar
When popping tabs out respect the "Open windows full screen by default" preference
Fix opening a collection when double-clicking an "Open this collection" file in the folder panel
Fix various minor visual glitches with the search dialog
Fixed a bug that resulted in text being clipped or ellided when using the Japanese translation
Fixed a bug that prevented a number of messages from being translated to Chinese or Japanese
Fixed a bug that prevented pasting into the search dialog query when viewing a chromatogram or an agarose gel
Fixed a bug where buttons could continue to be appear to be moused over after the mouse moves away
Files imported into an agarose gel or an alignment are now listed in the same order as in the folder view
Fixed a bug that sometimes prevented making selections on older macOS versions by disabling hiding the top toolbar
Ensure existing files with the same name are not overwritten when performing a contig assembly
Fixed a bug that sometimes prevented selecting the relevant amplified fragment when clicking a primer binding sites while viewing an agarose gel
Fixed a bug that prevented showing file icons for selected non-native files in the folder panel

New in SnapGene 7.0.1 (Jun 22, 2023)

Enhancements:
Added a 600 ms delay before the collapsed sidebar pops over on mouseover.
Reduced the visual footprint of the top toolbar
Added support for dragging files from the folder view into the simulate agarose gel dialog
Streamlined applying enzymes and primers to other agarose gel lanes by automatically switching the preparation method
Added a context menu to the search field in the search dialog
Improved presentation of searching and search results and links to all results in the search dialog
Improved tooltip for close tab buttons
Fixes:
Improved stability
Fixed various issues with selecting tabs
Fixed an issue that prevented reliably popping out tabs on macOS
Fixed an issue that made it difficult to close files on some read only remote volumes
Improved placement of menus when clicking kebab buttons so they do not extend off the screen or are shown in the wrong display.
Fixed a bug where the wrong document might be shown when selecting a tab if previously none were selected
Fixed an issue that resulted in broken aliases when importing a Vector NTI database
Fixed an issue that sometimes resulted in action dialogs not updating the product when a primer was modified
Fixed an issue that could result in a simulated product showing up blank in cloning dialogs
Fixed various issues with flagging terms with problems when using the search dialog
Fixed an issue where clicking suggested terms and examples could result in duplicate terms be inserted into the query
Fixed an issue that made it difficult to clear the query in the search dialog
Fixed an issue that prevented clicking the X buttons repeatedly without moving the mouse in order to quickly clear out recent documents and projects
Enable the top toolbar menu actions in the View menu when the Get Started pane is shown
Fixed a issue that prevented importing some Uniprot sequences if a similar sequence exists in the nucleotide database
Fixed an issue that could result in primers being added to the wrong document.
Fixed a bug that could result in the detect common features checkbox becoming unchecked when modifying the sequence in the New File dialog.
Improved stability when switching between documents in a collection.
Fixed a crash that could occur when simulating an agarose gel
Fixed issues various with using cut, copy and paste in the search dialog
Improved the positioning of the advanced search dialog
Fixed an issue that resulted in charms at the top left being clipped when the sidebar was collapsed on Windows
Fixed an issue where changing topology or strandedness in the New File pane resulted in the preview turning blank and detected features not being shown
Fixed varius rendering artifacts when viewing the Get Started pane with SnapGene Viewer
Fixed an issue where if multiple tabs with unsaved changes are open, the active tab was not always used in cloning dialogs
Fixed an issue that resulted in always opening standard cloning vector as a stand alone window instead of a tab
Ensure orientation controls in cloning dialogs work reliably
Improved text colors for status widgets in light and dark modes
Fixed an issue where export options for gels could be listed in the File menu after switching to other document types
Fixed a freeze when changing topology in the Design Synthetic Construct dialog
Disabled the Order Construct menu actions when viewing the Get Started pane
Prevent primer name conflicts when manually specifying primers in an agarose gel
Prevent primer name conflicts when applying primers to all lanes in an agarose gel
Fixed an issue where some buttons would show pliancy, suggesting they could be clicked, when the mouse was outside the button area.
Fixed a bug that could result in spaces being inserted into the query when switching to the advanced search dialog.
Improved link to learn more about how to manage your projects in SnapGene
Fixed a bug where when using the context menu to pop out a tab as a new window did not result in the window being active.
Fixed a bug where clicking the advanced search button on Windows did not result in showing the advanced search dialog, only the result results tab.
Fixed various issues with showning pliancy after popping out a window.

New in SnapGene 7.0.0 (Jun 8, 2023)

Features include:
Tabbed Interface
Search for files within the selected project folder based on file or sequence characteristics
Visualize Primer Annotations in the Add / Edit primer and selected cloning dialogs
Preview detected features when creating a new sequence
Get Started pane with easy access to learning resources + recent projects or files
Directly input selected files into alignments, assembly cloning methods and gel simulations based on the sequence selection in the folder panel.
Import multi-sequence files to a folder
Restructures primer dialogs to make it easier to insert into the primer sequence
Offer the option to insert a non-degenerate recognition sequence into a primer sequence in the primer dialogs.
Improved binding site information shown in the primer dialogs
Search for sequences in Dotmatics Bioregister directly from within SnapGene based on the sequence name, Bioregister ID, or using a similar sequence (BLAST search) Import and search Dotmatics Bioregister directly within SnapGene
Added support for changing methylation when simulating agarose gels
Improved first launch experience
Added ladders from Nippon Genetics
Modern look and feel
Easy and flexible file and folder management:
Choose any folder on your files system as a project
View subfolders and files list directly within SnapGene via new navigation panel
Quickly browse all SnapGene supported file types, including DNA, RNA, protein, alignments, chromatograms and gels
Perform standard file operations directly within SnapGene
Context-based quick links for easy access to common tools
Additional changes and fixes:
New option to apply primers to all agarose gel lanes
Added ability to extend the selection from a selected feature to an arbitrary position and vice versa
New option to automatically add upstream bases when inserting 5’ restriction sites into primers
Added support for undo and redo in the Add / Edit Primer dialog
Primer annotations created when insertions added automatically during cloning simulations
Added support for duplicating and editing imported codon usage tables
Added command line preview in RNA secondary structure settings
Adjusted the equation used when simulating agarose gels to provide more accurate results
Added warning for Collections top folder if it has a contents that will not be visible via SnapGene’s Collections UI
Added setting to hide legacy Collections functionality by default
Replaced Launch dialog with the ‘Get Started’ space
Improved look and feel of Windows installer on high resolution displays
Fixed issues with adjusting the endpoints of multi-segment features
Fixed an issue that could prevent adjusting the position of point features
Fixed an issue with garbled text and displaying the dates primers were added in Primers view
Cmd+W no longer closes the "Save Unsaved Changes?" dialog
Improved the FASTA importer to reject files that include numerical characters on non-comment lines
Fixed various issues that prevented opening some Geneious files
Added support for editing imported genetic codes and duplicating genetic codes
Fixed a bug where changing the reading frames shown in sequence view or sorting enzymes in Enzymes view had no effect on Windows or Linux.
Added TaKaRa DL500 ladder
Added a missing band to the Azura PureView 100 bp DNA Ladder

New in SnapGene 6.2.2 (Apr 12, 2023)

New in SnapGene 6.2.1 (Jan 11, 2023)

New in SnapGene 6.2.0 (Dec 8, 2022)

New Functionality:
Suboptimal RNA secondary structures
RNA structures can be recalculated using adjusted Tm and other settings
Display and make sequence selections in Structure view
Coordinates and 5' / 3' end labels can optionally be displayed in Structure view
Added menu actions at the top right of Structure view to reset pane, rotation and scale
Added a ligation fidelity matrix to the Golden Gate Assembly tool for assessing overall reaction fidelity
Cut a Golden Gate Assembly vector with any enzyme (not just Type IIS enzymes)
Adjust overhangs for manually designed primers while simulating Golden Gate Assembly
Adjust the hybridization region for all PCR cloning simulations. When using automatic primer design, the hybridized region will be configured automatically, ensuring miscellaneous features are not transferred to the product when a 5’ primer extension by chance partially hybridizes to the template.
Copy or export the properties and amino acid data for full protein sequences or selected regions
Copy individual protein properties
Enhancements:
Check for and prevent simulating Golden Gate assembly if two adjacent fragments are set to be used directly and abutting ends both lack 5' terminal phosphates
Improved the appearance of many icons on low DPI displays
Display the selected MW in the selection bar for protein alignments
Improved the error message shown when attempting to ligate linear fragments that lack 5' terminal phosphates
Updated the Golden Gate Assembly dialog to include easy access to recommended enzymes
Improved the default sequence name when pasting FASTA encoded sequences into the New File dialog
Modernized application, file, and various other icons
Added links to NEBuilder® HiFi DNA Assembly and TOPO® Cloning tutorial videos.
Show complementary bases of neighboring overhangs in Golden Gate cloning mini-overviews
Zoom to fit by default when viewing RNA secondary structures
Fixes:
Fixed an issue where quality of sequences aligned to a reference was sometimes not shown when requested
Improved the appearance of tab controls on macOS
Improved the appearance of slider controls on macOS and fixed an issue that prevented vertically scaling peaks for traces aligned to a reference sequence
Improved overall stability
Fixed an issue that prevented simulating Golden Gate cloning when a golden gate site blocked by methylation was present within the insert or in the assembled product
Corrected an issue where when exporting translated features that use a custom genetic code (e.g. Amber) to GenBank the /transl_table qualifier should be omitted and this information is encoded using a /note qualifier instead
Fixed issues with importing multi-sequence GenBank files that contain empty sequences (name only)
Fixed an issue where protein sequences were sometimes imported from NCBI as DNA or RNA when using the import extra features option
Fixed issues with selecting the codons just upstream and downstream of the site of ribosomal slippage
Fixed an issue that sometimes prevented aligning bases adjacent to internal mismatching regions
Ensure "Show History" is always a blue clickable link in textual representation of History view
Corrected the default methylation for newly created sequences to match the default strain specified in Preferences
Disabled the 3-Letter Amino Acids action in the sequence view context menu when using compact mode
Fixed a crash when detecting common features
Fixed an issue where quality data was sometimes not shown for all sequences aligned to a reference
Fixed an issue with stripping out some formatting when copy and pasting from web pages into the description panel or other rich text controls
Corrected an issue where feature colors were not accurately shown when using dark mode
Addressed a number of issues with creating features in protein sequences
Only allow a single copy of the alignment dialogs to be shown at a time
Fixed the horizontal alignment of the "Show as Uninterrupted Circle" button in the side toolbar
Do not show a cursor when clicking and holding on a codon in Sequence view
Avoid showing duplicate copies of open documents from the Window menu
Do not show a translation window when starting SnapGene on a computer configured to use a non-English locale such as German but one that the application is not translated into
Removed duplicate "site" feature type from the feature type cascading menu
Improve area printed when printing RNA structures
Fixed an issue where printed RNA structures were sometimes blurry
Fixed an issue where an I-beam cursor was shown when mousing over Sequence view in contexts where arbitrary selections cannot be made such as the Silent Mutagenesis dialog
Fixed an issue that prevented detecting the preferred language on macOS
Fixed an issue where the wrong number of binding sites was sometimes listed in cloning dilaogs when simplified binding sites were shown
Fixed an issue where primers designed automatically and those specified manually were not always shown annealing to the template in the same manner
Fixed various issues when using multiple screens.
Various textual corrections
Fixed a stability issue when attempting to use a linear fragment directly when simulating Overlap Extension PCR
Fixed an issue where the application would freeze when attempting to generate primers for Golden Gate cloning if the fragments already contained one or more sites for the Golden Gate enzyme.
Fixed issues where windows were not always shown on the logical display when using multiple displays on macOS.
Improved opening older Geneious files.
Fixed an issue where alternate transcripts (isoforms) were incorectly listed already in and thus not imported directly when importing features from another file.
Fixed an issue that could prevent batch importing features
Fixed an issue where when importing an enzyme list unknown entries were imported as AanI.
Fixed an issue where using the Choose Primers command would fail to design primers for linear vectors or fragments if you did not first make a selection. SnapGene now correctly designers primers to use the entire linear sequence.
Fixed a stability issue when changing the number of fragments to 1.
Fixed an issue where if the first or last fragment in Overalap Extension PCR was not amplified by PCR the forward and/or reverse primers for amplifying the assembled linear fragment were not configured automatically when using the Choose Primers command.
Fixed ordering from Vector Builder
Fixed the link for more information about fonts and printing on Windows
Improved rendering buttons and images when dragging windows between low and high resolution displays
Fixed various memory leaks
Fixed an issue where primers binding sites with melting temperatures less than 30 C were not identified
Improved the behavior of the Secondary Structure zoom control
Improved decoding feature types from Vector NTI databases
Removed the MAFFT penalty shift setting since it was problematic
Updated links to the user guide and user guide articles

New in SnapGene 6.1.2 (Oct 13, 2022)

New in SnapGene 6.1.1 (Aug 22, 2022)

New in SnapGene 6.1.0 (Jul 6, 2022)

New Functionality:
New Golden Gate Assembly simulation tool, either using existing Type IIS enzymes or through automated primer and overhang design
New Secondary Structure view tab for single stranded RNA sequences. Structures calculated using the ViennaRNA package
Added support for Dark mode, automatically using the OS settings for macOS and Windows
Native support for Apple Silicon machines
Enabled customization of content exported to GenBank including LOCUS field identifier and feature export options
Enhancements:
Added "Synthetic Protein" and "Unknown" options for the Source attribute in the description panel
Added DNA ladders from OriGene
Ladder fragment lengths are now displayed in the fragment list in agarose gels
Added LOBSTR to the list of E. coli strains
Improved the detection and simplified the display of primer hybridizations with 3' overhangs
Provide a cancel option when a message is shown indicating an unknown or not installed custom feature type must be addressed before proceeding with editing or duplicating one or more features
Added links to SnapGene Academy
Extensive optimizations
Various textual and layout enhancements
Fixes:
Improved stability
Fixed various memory leaks
Fixed issues with opening some GenBank files
Ensured the fragment list in cloning dialogs continue to refresh when either enzyme is manually cleared
Improved text spacing after punctuation characters on macOS
Fixed an issue that prevented the Enzymes view "Select Range" context menu command from working
Improved mouse pointer shape when over links in Collection windows
Fixed or improved various links to SnapGene.com pages
Fixed an issue where cloning dialogs could get stuck generating the product
Fixed an issue where some windows omitted the title bar on Windows
Fixed an issue where selected codons were not always shown using a white foreground in Sequence view
Fixed an issue where Ready to Clone was still shown after adding or removing a fragment, even if cloning was no longer possible
Use the default file format specified in Preferences when exporting alignments
Fixed an issue with Geneious file import where features in protein sequences could erronously be translated
Fixed an issue with Geneious file import where introns in nucleotide sequences imported were translated
Fixed an issue where the Enter key in the numpad was not responsive when a combo box or line edit had focus on macOS
Improved image quality when exporting to EMF format
Improved display of checkboxes on Windows
Fixed dropdown menus in Windows which sometimes had clipped text
Fixed issues with the display and behaviour of default buttons in dialogs
Fixed an issue with files appearing disabled in the macOS file explorer when they were able to be chosen
Fixed an issue that prevented pasting into the Find control in the Open and Save As dialogs on macOS
Fixed an issue that prevented importing AddGene sequences that contain reserved characters in the file name into a Collection on Windows
Corrected an issue that resulted in an incredibly wide window when importing a database from CSV format that lacks headers into a Collection
Fixed an issue where ancestral sequences that cannot be resurrected were shown as blue links in the text format of History view
Fixed an issue where the Add Primer command could add a primer to an open DNA window even if a Collection window was active when the command was triggered
Fixed an issue with the display of an amino acid selection highlighting within a translation
Fixed an issue on Ubuntu whereby AB1 files in a Collection opened in SnapGene Viewer if installed
Fixed some issues with dialogs opening in strange positions, such as on a different monitor
Addressed a stability issue when editing a collection description.
Fixed an issue with importing mixed content types from NCBI
Fixed various issues with the sequence name when importing from NCBI, especially when using the COMPLEMENT operator.
Fixed a number of printing issues on Windows when the operating system is set to scale all content to 100% or 150%.
Fixed the appreance of the transformation strand menu in the Change Methylation dialog on Windows.
Fixed printing the header for multiple sequence alignments on Windows using 100-200% scaling.
Improved printing margins on Windows.
Improved print quality of mutiple sequence alignments on Windows.
Imporved the default height of the Insert Codons dialog.
Improved the horizontal alignment of text in the fragmnets list shown in Agarose Gel documents.
Improved the display of site feature labels in multiple sequence alignemnts.
Fixed an issue where browsed or edited common features are not realible shown with all relevant qualifiers in the Browse Common Features dialog.
Repliably respect the "Detect either an exact protein match or approximate DNA match" setting when detecting common features.
Improved margins when printing on Windows
Fixed horizontal alignment of enzyme names when printing on Windows.
Addressed various issues when printing on Windows with the display scaling set to 200% or higher.
Improved the width of spinboxes on Windows.
Avoid elliding menu commands on Windows
Fixed various issues that made it difficult to install software updates on Windows.
Improved behavior of progress bar when when installing software updates on macOS.

New in SnapGene 6.0.6 (Jun 24, 2022)

New in SnapGene 6.0.5 (May 15, 2022)

New in SnapGene 6.0.4 (May 4, 2022)

New in SnapGene 6.0.3 (Apr 19, 2022)

Enhancements:
Impoved formatting when using the Copy Selected Primers and Export Primer Data commands.
(Requested by Di Xia)
Improved responsiveness of cloning dialogs when switching tabs and flipping fragments.
Improved responsiveness when making selections in multiple sequence alignments.
Improved responsiveness when performing or opening a file with an alignment to a reference sequence.
Fixes:
Fixed an issue with renaming folders in collections.
(Reported by Dinesh Babu Paudel)
Avoid switching from Map to Sequence view after importing sequences to align to the reference.
(Reported by Cary Valley and Michal Poborsky)
Fixed an regression where features in replaced regions were erronously retained during restriction cloning if the insert was the same size.
(Reported by Martha and James Smart)
Fixed an issue with decoding features from GenBank files generated by CHOPCHOP.
(Reported by Reuben Philip)
Fixed aligning sequences in a multi-sequence FASTA file with a reference.
(Reported by Fang Suo, Louise La Barbera Kastberg, Guttorm Haraldsen, and Ryan McNulty )
Fixed an issue with opening supported file types in Miscellaneous Files when viewing a collection.
(Reported by Dinesh Babu Paudel)
Fixed a default file name and extension when saving a sequence trace.
(Reported by Dinesh Babu Paude)
Addressed an issue where Sharepoint index conflict files resulted in new file notifications when working with collections.
(Reported by Andras Solt)
Improved stability when detecting common features.
Fixed an issue where the selection bar was blank after making a feature in a multiple sequence alignment.
Fixed a crash when attempting to create a custom feature type in SnapGene Viewer.
Fixed an issue that prevented loading non-installed custom feature types that are embedded within a file.
Improved stability with multiple sequence alignments.
Fixed a memory leak when creating, editing, or duplicating features.
Corrected an issue with history colors after performing PCR using primers that extend beyond the end of a linear template.
Fixed an issue with making RNA sequences from selections in large genomic sequences.
Fixed an issue where unnecessary menus were sometimes shown on the launch dialog.
Fixed various issues where characters right of a period in a agarose gel sequence name was not shown in the fragment list or source control
Removed unecessary message indicating upgrading to SnapGene is required to perform an alignemnt if one or more aligned sequences and an associated alignment to the reference sequence is already computed.
Improved overall stability
Addressed various memory leaks.

New in SnapGene 6.0.2 (Jan 17, 2022)

New in SnapGene 6.0.1 (Jan 13, 2022)

Fixes:
Improved stability when showing context menus in Sequence view.
(Reported by Yaocheng Li)
Fixed an issue where some mirrored files on Windows were not shown in collections.
(Reported by Philippe Malivert)
Retain the order in which files were selected when aligning them to a reference sequence.
(Reported by Echo Pan, Justine Grisez and Clifford Dustin Rubenstein)
Corrected an issue where selected feature types were not visible in the Manage Feature Types dialog on Windows.
(Reported by Stefano X Tonin)
Fixed an issue that could result in duplicate primer binding sites or binding sites shown at the wrong location.
(Reported by Haijuan Yang, Justine Grisez, Viktoria Lytvyn, Rhiannon Carr and Edward Green)
Added a warning if the maximum file path on Windows would be exceeded in order to convert a multi-sequence FASTA archive with very long sequences names to a Collection.
(Reported by Wulf Leuschner)
Fixed an issue where "Copy Top Strand Bases" was not shown when viewing a Collection.
(Reported by Mitchell Altschuler)
Sped up loading sequences in agarose gels.
(Reported by Liuqi Zhao)
Fixed the keyboard shortcut for find protein sequence.
(Reported by Tim Zhou and Anthony Picard)
Fixed an issue that prevented opening documents from Signals Notebook with non-Latin characters in their filename.
Improved stability when closing windows and quitting.
Fixed an issue where the application logo was clipped in the launch dialog on Linux.
Improve spacing of fragment controls in cloning windows.
Corrected messages in the New DNA/RNA file window that at time incorrectly indicate the topology of the sequence that will be created.
Fixed an issue where some pull down controls were too narrow on Windows.
Improved stability when mousing over stop characters (*) in protein alignments.
Corrected an issue where collection folders were at times expanded automatically by mistake.
Fixed a crash when trying to open a mirror to a mirror file in a Collection.
Fixed an issue with importing some PubMed references that include Unicode characters.
Fixed a stability issue when switching between sequence trace and other window types on Windows or Linux.
Fixed importing a Vector NTI Express database with an atypical Java installation.
Fixed an issue with printing genetic codes.
Fixed an issue where an agarose gel fragment list could be clipped on Windows.
Numerous other stability improvements.
Fixed an issue where feature annotations could be lost when adding a restriction site via silent mutation.
Corrected an issue that prevented detecting a converted or extended trial license.
Corrected an issue with clipped content at the top of the Keyboard Shortcuts and Gestures dialogs on Windows and Linux.

New in SnapGene 6.0.0 (Dec 2, 2021)

New Functionality:
Added a tool for adding enzymes sites to a coding sequence by silent mutation
Added a tool for removing an enzyme site from a coding sequence by silent mutation
Added support for custom features types not included in the standard set of GenBank feature types
Enabled changing the default color of standard Genbank feature types
Added support for saving and loading Agarose gel simulations as .gel files
Added support for features within pairwise alignments
Enabled adding, editing and deleting features in alignments
Added a features table when viewing pairwise and multiple sequence alignments
Enabled searching an alignment to find features
Enhanced Gibson, InFusion and NEBuilder HiFi Assembly simulation tools to allow the vector to be flipped
Enhanced cloning simulation tools to support adding, removing and re-ordering sequences
Included controls to filter the set of chosen enzymes based on the number of times and relative location an enzyme cleaves with respect to its recognition sequence
Enabled setting a default Codon Usage Table
Added tool for converting ng/uL to nM in the DNA Calculations dialog
Added base counts to the DNA Calculations dialog
Enhancements:
Enhanced the 'Blocks of 3' Sequence view format to enable aligning nucleotide triplets with the reading frame
Support for optionally displaying sequence names alongside the sequences when printing pairwise and multiple sequence alignments
Switched from "?" to "X/Xaa" in translations to represent ambiguous amino acids
Added Tm for the selected region in ssDNA sequences
Added a locking mechanism which sets files as read only to other instances of SnapGene when being edited. Note that the locking mechanism is not available on large files, and has short delay, so is not effective when files are opened simultaneously
Convert Psi to U when importing or creating a new RNA sequence
Added support for including binding site locations when exporting primer data
Added Gateway Cloning destination vectors pEXP3-DEST and pEXP4-DEST, and updated cross-references in descriptions for pEXP-DEST Vectors
Features and custom numbering are now retained when copying and pasting into the New Protein File dialog, or inserting or replacing residues in a protein sequence
Added support for pasting copied complementary primer pairs to configure an Agarose Gel lane
Improved explanation for how to change sequence methylation when an enzyme is blocked during Restriction Cloning
Added support for adjusting the resolution (ppi) and creating a transparent image when exporting maps from the command line interface
Included various textual enhancements
Fixes:
Included Nicking enzymes in the 6+ Cutters enzyme set
Remove secondary recognition sequence for TaqII as this does not result in cleavage
Restore last shown enzyme variant when returning to a previously viewed enzyme in the Restriction Enzymes window.
Reduced file size and sped up loading files by omitting features in History view for large ancestral sequences
Added support for the following non-standard qualifiers for all translatable feature types: calculated_mol_wt, codon, codon_start, exception, protein_id, transl_except, transl_table, translation
Non-standard qualifiers are now retained when importing and exporting (previously they were converted to /note)
Added support for /transl_table and /codon_start qualifiers with CDS features in protein sequences
Fixed an occasional issue on macOS where an empty SnapGene window appears which cannot be closed except by restarting SnapGene
Disabled subsidiary check boxes when appropriate in Preferences
Corrected mouse-over effects for Site features with multiple segments
Fixed an issue that prevented setting a protein point feature type to misc_feature, unsure, or variation.
Automatically change feature color when changing the type when adding a point feature if the color has not been manually adjusted.
Fixed an issue where U's were not converted to T's if either end of a linear DNA sequence is modified to be covalently closed.
Fixed an issue where unsaved files added to the align sequence tools were listed using the wrong name
Fixed an issue that sometimes prevented run-on translations from being shown in alignments
Ensured it is always possible to scroll to the last base in DNA files
Removed inappropriate methylation message which was shown when opening the features tab for some protein files
Corrected an issue that prevented pliancy from being shown when using the "Choose Alternative Codons" tool
Corrected various display issues when switching a lane in an agarose gel simulation to using a MW marker
Fixed an issue that prevented point features from being added to protein sequences
Require a product name to be specified when using the Mutagenesis tool
Ensured bases are always visible when history colors are shown
Always show shared codons in adjacent translated features within Sequence view
Fixed Align to Reference DNA sequence so that undoing sequences edits no longer hides the aligned sequences
Reliably display ORF's that wrap around the numerical origin in circular sequences
Fixed an issue that prevented some keyboard shortcuts from working while the launch dialog was visible on Linux
Correctly show the Description Panel by default when this preference is toggled on
Ensured the navigation buttons in the Choose Alternative Codons tool are properly enabled
Corrected an issue with searching for features in protein sequences when Region features are not shown
Fixed an issue where qualifier selections in Features view were lost when switching tabs
Fixed an issue where using undo while viewing an alignment to a reference sequence resulted in expanded aligned sequences being collapsed.
Fixed issues with Make Protein and Copy Translation with two abutting in-frame translated Features for which a codon spans the feature boundaries
Fixed lagging selection of checkboxes on windows when importing primers
Enabled jumping to next/previous regions across the origin using "Next/Previous Aligned Region" buttons
Clarified dialogs to indicate Java 8 is supported for Vector NTI Express database import
Fixed the default folder in Preferences > Files for opening being ignored by Open Files
Corrected an issue that resulted in primer names not being included in default document name when creating a new file from a primer pair selection
Fixed an issue that prevented using the NEBuilder tool with primers that are separated by less than 50 bp
Corrected an issue with refreshing the list of sequences after clearing the search control when using the Import SnapGene Online Sequences tool
Fixed an issue that prevented using preexisting non-overlapping PCR primers for the vector when using the NEBuilder tool
Corrected an issue that prevented dragging and dropping files onto Agarose Gel windows
Corrected an issue that prevented shown chosen enzymes when switching between documents in a collection
Removed unnecessary horizontal lines that remained after removing references in the Edit References window
Improved default size of the Edit References window
Corrected an issue with displaying the selection length for selections with sticky overhangs
Improved stability when making selections in sequences aligned to a reference
Removed ambiguous codons when using the Insert Codon and Choose Alternative Codons tools
Improved stability when using Opt-click to close all files
Improved overall stability and corrected various memory leaks
Restore selected history operation and display of history colors after undoing hiding an operation.
Corrected an issue where an erroneous message was shown indicating a purchase was required before installing an available software update.
Improved the name and icon shown for alignment documents in Window menus
Fixed an issue that prevented correctly displaying where sequences align to a reference sequence in Map view.
(Reported by Lauri Lintott)
Improved the appearance of simulated agarose gels on screen and when exporting to a file
Improved stability when saving multiple files in a collection
Improved the appearance of site features in linear maps when printing and copying to the clipboard.
Ignore collection index conflict flies created by OneDrive.
(Reported by Andras Solt)
Fixed an issue that prevented using selected primers to pre-populate controls in PCR-driven cloning dialogs.
Fixed position where the add/edit/duplicate protein feature dialogs appear
Improved stability when clicking on Save to Main Collection without a file selected
Correctly display the sequence name above enzyme sets that are associated with a single sequence in the side toolbar menu
Stability fixes when using splice to remove intros and new file from selection
Fixed wrong shortcut showing on Windows in search type combo box for search bar (Meta→Alt)
(Reported by Michael Lynge Nielsen)

New in SnapGene 5.3.2 (Jul 8, 2021)

Fixes:
Corrected an issue with showing aligned sequences as double-stranded DNA.
(Reported by Christine Chidester, Lauren Flynn, and Clifford Dustin Rubinstein)
Addressed an issue with folders in collections stored on network drives.
(Reported by Stefan Kalies)
Addressed a stability issue with viewing some primers in Sequence view.
(Reported by Ferdinand Greiss)
Ensured correct reporting of the number of matches when searching ssDNA sequences.
(Reported by Jeff Sekelsky)
Fixed a regression that prevented the display of some primer binding sites when simplified hybridizations are being shown.
(Reported by Katjusa Brejc)
Increased the number of primer binding sites that can be shown in Map view.
(Requested by Jadyn Cox, Hsinho Huang, and Sara Smith)
Fixed an issue that sometimes prevented showing the first aligned sequence when printing an alignment to a reference sequence.
(Reported by Daiki Matsuda)
Corrected an issue with saving aligned reads to an ssDNA sequence.
(Reported by Daiki Matsuda)
Improved stability when expanding sequences aligned to a reference DNA sequence.
(Reported by Scott Brown)
Improved stability when choosing alternative codons.
Ensured that opened documents are always added to the recent files list.
Fixed an issue that could prevent enzymes from being displayed in older documents in collections.
Ensured that display options are always preserved when duplicating collection documents in a new window.
Removed a blank cascading menu that could appear in the Edit menu when using "Save As".
Improved stability when dragging trimming handles.
Improved stability when using Opt-click to invoke "Close All Open Files" on macOS.
Improved the appearance of the focus ring for comboboxes on macOS.
Improved the mnemonic shortcut for deleting a restriction fragment on Windows.
Improved the default filename when exporting an alignment.
Improved colors in cloning overviews.
Made various textual corrections.
Prevented unnecessary scrolling when undoing sequence modifications.
Improved stability when using short sequences aligned to a reference DNA sequence.
Improved stability when using "Splice to Remove Introns".

New in SnapGene 5.3.1 (Jun 9, 2021)

Fixes
Ensured retention of unchanged alignment name and omission of name controls when using the "Replace" option when redoing an alignment.
Fixed an issue where File → Save did not work after redoing an unsaved alignment.
Preserved the display of preferred codons when switching between DNA and mRNA formats when viewing a codon usage table.
Allocated sufficient space to display the "Size" column in Features view when viewing ssDNA and ssRNA sequences.
Prohibited pasting when multiple files are selected in a collection.
Prevented a crash that would occur after double-clicking when importing SnapGene and Addgene online sequences.
Completely removed the installation folder when uninstalling on Windows.
Enabled "File → Export → Alignment..." and "File → Export → Consensus..." when viewing an alignment.
Made significant stability improvements.
Reduced memory usage.
Improved date formatting on Windows.
Improved button placement in History view.
Fixed an issue that could cause custom common features to be corrupted by using the right-click context menu to edit a common feature.
(Reported by several users)
Removed the "Hybridization Parameters" menu action when viewing an RNA sequence in a collection.
Improved manual adjustment of vertical scaling of sequences traces aligned to a reference sequence.
Fixed an issue that prevented importing from Vector NTI databases on Windows.
(Reported by Dunhua Zhang)
Addressed an issue with importing some Vector NTI Express databases.
(Reported by Max Fu)
Fixed an issue in which the text representation of History view did not always refresh immediately when edits were made or undone.
Ensured correct enabling and disabling of the "Edit History" control in History view when the history is modified.
Corrected an issue that allowed duplicate primers with the same name but different sequence case to be imported into a file.
Corrected various issues that could occur when attempting to add features to the common features database, or importing such features, if they were marked as not visible in the original document.
Ensured correct export of common features to the specified folder.
Addressed issues that prevented collections stored on Windows network shares from being listed as recent collections in the File → Open Collection menu.
Improved fonts and text placement in History view.
Improved the message shown if an alignment is selected in a collection.
Corrected an issue that could cause pop-up menus to remain open when the Launch dialog was closed.
Corrected an issue that prevented saving a new file created from a selection from being saved to an open collection.
Ensured remembering of a preference for showing additional binding sites that do not match at the 3' end.
(Reported by Dan Piraner)
Corrected a regression that prevented imported primers from being restricted to those that have a unique binding site.
(Reported by Lauri Lintott, Michal Dolezal, and Jadyn Cox)
Ensured that the chosen enzyme set and enzyme visibility are retained when undoing sequence edits.
(Reported by Scott James)
Ensured that bold is correctly used to highlight unique cutters after undoing sequence edits.
Reduced the file size when exporting maps and history as PNG images.
(Reported by Xavier Danthinne)
Improved the toggling of enzyme visibility when repeatedly clicking check boxes in Enzymes view.
Fixed an issue that prevented looking up an enzyme by right-clicking in the Enzyme or Sites column in Enzymes view.
Fixed an issue that incorrectly suggested a sequence trace has unsaved edits after using File → Save As.

New in SnapGene 5.3.0 (May 14, 2021)

New Functionality:
Added support for viewing features in multiple sequence alignments.
Enhanced History view with a Text format tab, and with an option to show the entire history.
Added support for RNA sequences as .rna files.
Enabled viewing files of all types simultaneously in a Collection using a new "All Files" area.
Enabled gaps to be displayed every 10th base for protein sequences, and every 10th or 3rd base for nucleotide sequences.
Added support for filling in DNA ends of annealed oligos to create a double-stranded DNA sequence.
Added support for annotating primers that anneal at the 5’ end but not the 3’ end.
Enabled viewing and printing chromatogram files in a wrapped multi-line format.
Improved the conversion of .geneious nucleotide and protein sequences and alignments.
Added DNA Ladders from Ecogen, TIANGEN, and Vazyme.
Enhancements:
Extended the range for the minimum required 3' match for primers from 25 to 35 bases.
Enabled export of alignments to rich text format .rtf files.
Enhanced the visualization of mutagenesis simulations and mutagenic primers.
Enhanced the response to mousing over a primer so that the binding site is now highlighted in gray.
Added support for /protein_id qualifiers for mat_peptide features.
Enabled printing to PDF on macOS when no printers are installed.
Added an indicator in the selection bar to show "DNA" or "RNA" as the sequence type.
Enhanced enzyme, feature, and primer label layout in Map view for linear sequences.
Added clickable "contact support" links to messages that pop up in various places.
Made terminator features directional in the common features database.
Added the keyboard shortcuts Cmd+1 / Cmd+2 / Cmd+3 for switching between tabs in chromatogram windows.
Enhanced cursor placement, highlighting, and trace data tooltips when the mouse cursor is between bases.
Changed the "Replace" button label in Collections to "Bulk Edit" for improved clarity and accuracy.
Improved primer binding sites to avoid bulges if a 5' N tail is present in the primer sequence.
Updated the MAFFT aligner to version 7.471.
Updated the Parasail aligner to version 2.4.2.
Added a shortcut (Shift + Spacebar) for scrolling one page up in multiple sequence alignments.
Streamlined toolbar on macOS.
Fixes:
Rationalized the View menu to show options relevant to the file type.
Removed the "Browse..." menu action that had no effect in the "Import Primers from a SnapGene File" dialog.
Adjusted the tooltips for buttons in the "Find" bar to make them more consistent with other tooltips.
Changed the heading in the Collection search dialog for Protein Files to say "Names" rather than "Names & Numbers".
Ensured that only a single /mod_base qualifier is allowed for modified_base features.
Added a ruler for protein sequences when viewing in compact format.
Fixed a bug with selection of the last item in Features, Primers, and Enzymes views.
Implemented immediate update of the version listed on the account administrator page after SnapGene is updated.
Corrected a regression in which sequence selection was lost after clicking in the Description Panel.
Corrected a regression with enzyme site selection in Lines mode of Enzymes view.
Ensured consistent display of the selection when switching to Sequence view.
Fixed an issue in which spaces were not shown after commas on macOS Big Sur.
Fixed a non-functional "Choose Enzymes..." command in the "Choose enzyme set" dropdown menu.
Corrected a regression that caused overtyping of characters in the primer name fields of the Simulate Agarose Gel dialog.
Ensured correct refreshing of primer binding sites when changing hybridization parameters.
Prevented truncation of 3' overhangs that extend beyond the end of a circular sequence.
Prevented input of an invalid location in the Go To dialog for sequences aligned to a reference DNA sequence.
Fixed some tabs that displayed as white text on a white background on macOS Big Sur.
Ensured that features are not lost from inserts in cloning operations when windows are opened or closed.
Corrected the color of the gray bar below the list box in the Collection interface.
Prevented "< Please choose >" from being propagated from the Anneal Oligos dialog to the oligo names in the resulting history.
Ensured that in the Anneal Oligos dialog, a double-click on a compatible enzyme is needed to transfer focus to the Restriction Enzymes dialog.
Configured the pull-down menus in the Anneal Oligos dialog to refresh when documents are opened or closed.
Ensured that the specified font size is used when printing the Description Panel.
Fixed an issue with the folder location used when exporting standard common features.
Improved scrolling performance in Enzymes view.
Fixed the default file name chosen when exporting a single file from a Collection.
Improved the reliability of displaying the warning in the Print dialog on Windows about printing to PDF.
Ensured that tabbed window controls on macOS are reliably shown.
Improved the background color display in Map view.
Fixed issue in which keywords could be used as the construct name for some GenBank/GenPept files.
Improved the opening of SeqBuilder files.
Addressed issues with importing references from another file.
Improved the quality when exporting maps at high resolutions.
Updated Map, Sequence, and other views when protein sequences are zoomed.
Implemented hiding of zoom controls in a collection when switching from a long sequence that supports zooming to a shorter one that does not.
Prevented unnecessary display of a message about unsupported qualifiers during NCBI import when the content includes nonstandard qualifiers (e.g., /UniProtKB_evidence) that are deliberately converted to /note qualifiers.
Corrected an issue in which some line breaks in /note qualifiers were not preserved when opening GenBank or GenPept files.
Addressed a potential stability issue when viewing protein files.
Fixed copying of maps and histories on macOS, and improved the quality when pasting such content into applications such as Microsoft Word or PowerPoint on macOS.
Improved the message shown when attempting to use a sequence over 1 Mbp to compute a pairwise alignment.
Ensured correct identification of macOS Big Sur when sending anonymous user statistics.
Ensured correct display of a trace file icon in the Windows menu.
Fixed various issues with specifying and displaying the /collection_date qualifier.
Addressed an issue that could result in sequence characters moving slightly after periods of no mouse activity on Windows and Linux.
Simplified the choice of a destination folder during import into a collection by making the "Add" button the default.
Improved the display of feature names on Windows during pliancy and selection.
Fixed the Redo shortcut on Linux.
Improved margins and alignment in various windows and dialogs.
Improved the default placement of a window created via File → Open when no document was previously open.
Improved stability while viewing collections.
Avoided duplication of DNA documents in the Window menu after converting to single- or double-stranded format.
Corrected the shortcut for Overlap Extension PCR of two fragments.
Ensured that if the side toolbar button is used to show alignments and there are no currently aligned sequences, the software asks which files to import to align to the reference sequence.
Corrected an issue in which unmodified alignment documents sometimes indicated unsaved changes.
Corrected issues with dragging collection files onto other applications.
Fixed a crash when saving an alignment to a collection.
Disabled "Actions → Convert to Single-Stranded..." when viewing alignments.
Corrected an issue that prevented conversion of a feature translation to upper- or lowercase if the last selected codon was located at the end of the sequence.
Fixed a bug in which an open document might not be listed in the Window menu or in the lists of open documents in cloning dialogs, while the launch dialog would remain visible.
Fixed an issue that could result in two copies of the application running on macOS.
Ensured correct rendering of multi-region Site features that span multiple rows in Sequence view.
Addressed a stability issue when exporting and opening the alignment consensus.
Removed the dead "Browse..." action in the source menu when importing features from BED, GFF3, or GTF files.
Ensured that "Primers → Sort Primer List..." executes the desired sort.
Updated outdated web links to online resources.
Ensured correct residue numbering for Smith-Waterman (local) pairwise alignments.

New in SnapGene 5.2.5 (Apr 27, 2021)

New in SnapGene 5.2.4 (Dec 17, 2020)

New Functionality:
Added DNA ladders from GeneBio Systems. (Requested by Dan)
Fixes:
Improved application stability when dragging out selections.
(Reported by Kengo Adachi and others)
Corrected a regression to ensure detection of restriction sites whose recognition sequences span the numerical origin.
(Reported by Anthony Picard)
Populate the "Description" fields when pasting GenBank content into the New File dialogs.
(Reported by Dustin Rubinstein)
Improved the detection of sequence type when importing DNASTAR SeqBuilder files.
(Reported by Oleh Rymarenko)
Corrected a regression to restore transfer of primers when pasting a copied DNA sequence.
(Reported by Peter Diebold)
Fixed an issue that could result in editing-induced disappearance of a sequence aligned to a reference DNA sequence.
(Reported by Paula)
Enabled simulation of Gateway BP and LR recombination around the numerical origin.
(Reported by Matthew Sale)
Improved application stability when searching for enzymes, features, and primers.
Corrected a misleading message that was shown when a problem occurred during program activation.
Ensured that the enzyme set indicator does not occlude content after scrolling to the bottom of Sequence view.
Streamlined the side toolbar in the Insert Codons, Choose Alternative Codons, Browse Common Features and Insert Feature dialogs.
Restored highlighting of the called base under the mouse when viewing sequence traces.
Improved application stability when using the "Find similar DNA sequences" command.
Improved performance when showing the Add Primer dialog and other dialogs that provide controls for choosing files.
Ensured highlighting of the inserted region for Gateway BP cloning in the Insert tab, and of the ancestral insert in History view for the resulting product file.
Restored import of ssRNA sequences as double-stranded rather than single-stranded DNA.
Prevented repetitive alignment to a reference sequence when making simple edits such as insertions, deletions, and same-size replacements.
Ensured that the Next button is the default control after searching a sequence trace.
Ensured correct scrolling of Sequence, Features, and Primers views in response to a change in the selection, but only when appropriate.
Improved application stability when quitting.
Improved application stability when hovering over aligned sequences.
Improved application stability when mousing over features.
Improved application tability when searching a collection for a named feature.
Improved application stability when importing primers.
Improved reliability when importing from NCBI.

New in SnapGene 5.2.3 (Nov 26, 2020)

Fixes:
Corrected a regression to enable the "Copy" command when a portion of an aligned sequence is selected.
(Reportd by Jai Padmakumar)
Corrected an issue that could prevent protein search results from being shown.
(Reported by Renato Lemgruber)
Improved the size and placement of the License Agreement and Align Multiple Sequences windows.
(Reported by Brian Tooker)
Ensured proper opening of GenBank files that omit the molecule type in the LOCUS line.
(Reported by Oliver Coleman)
Fixed an issue that could prevent using a attR Gateway site that lacks an optional leading nucleic acid.
(Reported by Robert Bill)
Fixed an issue with using Gateway fragments whose junctions lie at or very near the numerical origin.
(Reported by Robert Bill)
Ensured that files and collections located on network drives are included in the Open Recent File and Open Collection menus.
(Reported by Katherina Witte)
Fixed various glitches with displaying codon and ORF selections in Sequence view.
(Reported by James Scott)
Improved the appearance of tabs on macOS 11 Big Sur.
Corrected a regression to ensure auto-scrolling in Sequence view for selections made using the minimap or another view.
(Reported by Stuart Cahalan, Scott James, and Théo Grebert)
Corrected a regression to ensure display of restriction sites in sequences aligned to a reference DNA sequence.
Fixed an issue that resulted in ORFs sometimes not being shown.
Ensured that "Find" matches remain highlighted after switching away from and then back to Sequence view or Map view.
Ensured that "Find" matches are shown after restoring the "Find similar DNA sequences" controls.
Ensured that palindromic "Find" matches are highlighted in both strands.
Ensured proper display of "Find similar DNA sequences" matches that wrap around the numerical origin.
Improved the behavior of the search box in the Choose Enzymes window when searching for a noncutter while the "Hide noncutters" checkbox is checked.
Fixed an issue with detecting Gateway sites that have been customized by the user.
Fixed an issue with annotating Gateway sites that lie near the numerical origin after performing BP or LR cloning.
Ensured reliable import of features from SwissProt files.
Ensured reliable opening of SwissProt files that contain limited header information.
Corrected a regression to force use of the correct font in the New DNA File and New Protein File dialogs.
Ensured accurate display of multiple sequence alignment file names in the Window menu on Linux.
Improved reliability when installing software updates on macOS Big Sur.

New in SnapGene 5.2.2 (Nov 6, 2020)

New in SnapGene 5.2.1 (Oct 30, 2020)

New in SnapGene 5.2.0 (Oct 14, 2020)

New Functionality:
Enabled visualization of GC content as a color plot in Map view or base colors in Sequence view.
(Requested by Michael Brooks, Max Garwood, Robb Stankey and others)
Added support for finding similar DNA sequences with mismatches or indels compared to the search query.
(Requested by multiple users)
Added support for simulating the migration of supercoiled DNA molecules in agarose gels using TBE, TAE or SB buffer.
(Requested by multiple users)
Added support for single-stranded DNA (ssDNA) sequences.
(Requested by John O'Brien and others)
Enabled import of Sequencher project files (*.spf).
(Requested by May Cindhuchao, Heather McFarlane, and Usua Oyarbide)
Enabled "Undo" for edits in large sequences.
Added DNA ladders from DyneBio.
(Requested by Dae-Geun Song)
Added supercoiled MW markers from ELPIS BIOTECH and New England Biolabs.
Added BsmBI-v2 to the list of enzymes available from New England BioLabs.
Added fields for username and email address in the license registration dialog.
Enhancements:
Optimized storage of history for the following operations: Change Methylation, Change Transformation Strain, Set Origin, Flip, Insert/Delete/Replace, Linearize, Circularize.
(Requested by Dan Lysko, and by others who complained about large files)
Updated the supported protein feature types by adding new types (NonStdRes, Protein, Precursor, SecStr, Het, CDS, gene, misc_feature, unsure, variation), promoting Region subtypes to types, and adding new Site and Bond subtypes.
(Requested by Sanofi)
Added a note in Features view to indicate the presence of internal stop codons in a translated feature.
(Inspired by Tom Hamer)
Enhanced the Preferences tools to allow more flexible default options for displaying ORFs.
(Requesed by Caroline Reiss)
Enabled carrying over feature qualifiers when creating a protein sequence using "Make Protein" or "Reverse Translate".
(Requested by Katherine Geromini)
Added the option to merge segments when using "Make Protein" on a multi-segment DNA feature.
Added a "Hide noncutters" check box in the Choose Enzymes dialog.
(Inspired by Bruce Lahn)
Enabled importing features from any supported file type when using "Import Features from a SnapGene File".
(Requested by Greg Perry)
Enabled more flexible batch conversion of chromatogram traces to other formats.
(Requested by Arthur Fridman)
Improved search performance for large DNA sequences.
Configured the minimap to show both scrolled areas when two copies of Sequence view are visible.
Updated the format of the Preferences dialog, and added an "Agarose Gels" tab.
Added the option to designate a new collection as the Main Collection.
Enabled saving imported online sequences directly to a collection.
Added shortcuts in a collection Overview for navigating to the DNA Files, Protein Files, or Miscellaneous Files sections.
Enabled symbols to be entered in search queries when searching SnapGene Online Sequences.
Increased the size of the length indicator in the map label at the "Small" font size.
Consolidated all Fisher MW Markers for agarose gels in the Fisher Scientific set.
Configured the Nonredundant Commercial enzyme set to include similar enzymes that differ by methylation sensitivity.
Configured SnapGene to show the Launch dialog on macOS when the SnapGene icon in the Dock is clicked, if no SnapGene windows are open.
Changed the icon for enabling interrupted circle format for a linear DNA sequence in Map view.
Configured the "Export Map" and "Export History" options to be always enabled.
Improved the wording of various menu options and dialogs to provide greater clarity and consistency.
Added a message informing the user that files can be dragged into the list when using Align Multiple Sequences.
Fixes:
Fixed an issue that prevented cloning dialogs from allowing the use of hidden enzymes.
(Reported by Mily Ron)
Corrected an issue in "Protein Search" whereby terminal stop codons were not included in the search query.
(Reported by Mike Xie)
Ensured that edits in an alignment window do not cause inappropriate scrolling.
(Reported by Beth Lawrence)
Corrected an issue that could prevent alignment of a high-quality sequence trace.
(Reported by Jessie Saul)
Ensured that the "Find" control in the Enzymes view chooser always shows a message to indicate if the enzyme is not in the chosen set.
Corrected an issue in which U's in overhangs resulting from linearizing were not preserved.
Configured "Select All" in the trace viewer context menu to actually select all.
Ensured that History view reflects changes after editing DNA ends.
Ensured that case changes in the "Find" entry field are preserved when the search is executed.
Ensured that imported RNA alignments are converted to DNA rather than protein alignments.
Corrected the license inactivity countdown to displays seconds rather than milliseconds.
Ensured that the "Accession Number:" label remains next to its entry field in the collection Search dialog.
Ensured that a "Sequence Name" search in the Protein Files area of a collection also searches the map labels and aliases.
Corrected an issue that resulted in alignment and collection windows not showing unsaved changes in the title bar on Windows and Linux.
Ensured more consistent sorting of enzymes in the Choose Enzymes dialog.
Streamlined the substitution matrix options presented when computing pairwise alignments.
Ensured that open alignments can be used as profiles when computing new alignments.
Corrected an issue that could result in the "Kind" column disappearing when viewing a collection.
Ensured that crisp screenshots are shown when detecting updates.
Improved import of the full publication date from PubMed.
Made various stability fixes.

New in SnapGene 5.1.7 (Sep 23, 2020)

New in SnapGene 5.1.6 (Sep 17, 2020)

New Functionality:
Added Agilent TapeStation ladders.
(Requested by Gavin Johnson)
Fixes:
Corrected a regression that prevented decoding of features in Gene Construction Kit files.
(Reported by Matthew Mulvey and others)
Corrected a regression that prevented the bacterial transformation strain from being applied to the cloning product.
(Reported by Kengo Adachi)
Fixed an issue with applying the "Limit file history" preference.
(Reported by Michael Taschner)
Improved detection of Gateway attR1, attR2 and attR4 sites.
(Inspired by Mily Ron)
Improved the default binding site shown when invoking the Edit Primer dialog for a primer with multiple binding sites.
(Reported by Karim Hyder)
Corrected an issue with simulating Gateway cloning using att sites that lie across the numerical origin.
(Reported by Dominic Esposito)
Removed an outdated comment regarding PmlI losing activity when stored at -20°C.
(Reported by Wael Tadros)
Corrected the Import Primers dialog to proceed when Enter/Return is pressed.
(Reported by Stuart Cahalan)
Fixed an issue that could result in peak data disappearing when editing Sanger sequence traces.
(Reported by Dale Cowley)
Corrected a regression that prevented Shift-selecting a range of primers in Primers view.
(Reported by Dan Kraut)
Removed the "Fixed Line Width" button from the side toolbar in the Anneal Oligos dialog.
Corrected various stability issues when using cloning dialogs.
Ensured that the Sequence view minimap is consistently shown.
Fixed an issue with migrating the chosen enzymes when cloning while using a custom local enzyme set.
Corrected a regression that could cause the Browse Common Features dialog to switch from Sequence to Map view when the displayed feature was changed.
Improved the tooltips for history operations.
Ensured that changing the sequence methylation reliably updates the methylation state in the Description Panel.
Improved the document icon for DNA alignments to include a shadow.
Corrected an issue with splitting the view after having previously done so.
Corrected an issue with using Shift and the Left/Right arrow keys to move selected ranges across an entire gap in an alignment.

New in SnapGene 5.1.5 (Jul 21, 2020)

New Functionality
Added a "Copy Rich Text" command for selections in alignments, to provide the option of copying either simple sequences or sequences with metadata.
(Inspired by Leigh Harty and Nelson Ramirez)
Enhancements
Added Invitrogen's "pScreen-iT LacZ-Dest" to the list of Gateway® Destination vectors.
(Requested by Aysegul Gungor)
Modified the statistics in pairwise alignments to show two digits after the decimal point instead of one.
(Requested by Robin Luo)
Added time estimates to various progress dialogs.
Improved the order of "Copy" actions in the Edit menu.
Made various textual, alignment, and spacing improvements.
Enabled export of a map or history while viewing any tab.
Fixes
Ensured reliable import of primers copied to the clipboard using Microsoft Office.
(Reported by Daryl Beckford)
Added support for dragging and dropping FASTA archives into the Assemble Contigs dialog.
(Reported by Thomas Reinard)
Preserved zoom and split view display options when switching between files in a collection.
(Requested by Joon Park)
Enhanced the Gene Construction Kit importer to capture the full set of notes in the "General Info" section.
(Reported by Steve Stippec)
Improved stability when computing and viewing multiple sequence alignments.
(Reported by Leigh Harty)
Corrected an issue that could cause features to be erroneously detected around the numerical origin of a linear sequence.
Ensured that proper file extensions were included when batch converting files from one format to another.
Ensured correct setting of the default button in the Find controls when pressing and releasing Shift in a sequence trace window.
Corrected a regression with the navigation buttons when viewing an alignment to a reference sequence.
Addressed issues with the purple bar and the Tm column when importing primers from another file.
Corrected the displayed molecular weight when adding a translated feature to the common features database.
Removed the colors button in cloning dialogs, and streamlined the side toolbar in the Edit DNA Ends, Browse Common Features, and Mutageneis dialogs.
Improved the display of long sequence names within circular maps.
Corrected a regression by removing cut locations for ancestral restriction sites in History view.
Removed the inappropriate "Preserve feature annotations" control from the New File dialog, and the inappropriate "Detect common features" control when inserting or replacing bases in a sequence trace window.
Improved stability when assembling contigs using FASTQ data.
Disabled the Show/Hide All Enzymes commands when viewing protein files.
Corrected an issue in which the endpoints of a selection were not updated in the selection bar after renumbering the origin of a linear sequence.
Fixed an issue that prevented immediately using SnapGene without restarting after activating a Flexera-based shared license.
Corrected an issue with computing % GC when partially degenerate residues
(B, D, H, and V) were present.
Ensured that only the zoomed region is shown for the root map in History view.
Addressed an issue in which the Save As dialog would vanish immediately when attempting to choose a different name instead of saving over an existing file.
Ensured that enzyme set menus are refreshed after using Manage Enzyme Sets.
Ensured that the desired endpoint modifications are correctly applied when designing a synthetic construct.
Improved the registration of file associations on macOS.

New in SnapGene 5.1.4.1 (Jun 22, 2020)

New in SnapGene 5.1.4 (Jun 18, 2020)

New Functionality:
Added support for importing protein features from the GFF3 format.
(Requested by Takeda)
Enabled features to be preserved when a replacement leaves the sequence length unchanged.
(Requested by Sanofi)
Enhancements:
Enabled the import of custom user fields from Vector NTI databases.
(Requested by Decheng)
Increased the 3' match length limit to 25 bases when importing primers from a list.
(Requested by Yield10 Bio)
Enabled capture of the history of a protein translated from DNA when importing from Vector NTI Advance.
(Requested by Romain Merceron)
Enhanced primer tooltips to include % GC for the annealed region.
(Requested by Ori Mayer)
Improved copy and paste of sequence alignments into text editors and other programs.
(Requested by Pam Cook)
Increased the size of the DOI field when editing references.
Made various color, layout, and textual enhancements.
Fixes:
Mandated use of the proper default font size when creating new files, importing from online, and opening non-native files.
(Reported by Donelson Smith)
Corrected an issue that prevented importing primers into multiple files in a collection.
(Reported by Michael Brasino)
Corrected a regression with displaying translations and the "Original Sequence" when no sequences are aligned to the reference DNA sequence.
(Reported by Scott James)
Enabled changing methylation for placeholder files.
Fixed various issues when working with placeholder files.
Implemented automatic correction of invalid alignments to a reference sequence computed with prior versions.
Fixed an issue that prevented manually specifying the zoomed range.
Corrected the "+" symbol in plasmid names when importing from "SnapGene Online Sequences".
Ensured correct updating of the zoomed range when navigating to matches with the Find tool.
Addressed an issue with specifying the position of protein interchain bond locations.
Removed the "Codons" cascading menu when interacting with protein sequences.
Corrected an issue that prevented importing multi-sequence GenBank and GenPept files into a collection.
Ensured that translation numbering is maintained when using Make Protein from multiple selected translated features.
Ensured that the match threshold controls are listed only once when importing features from a SnapGene file.
Corrected an issue that could cause file names to be clipped in source menus.
Fixed an issue that caused files to be marked as modified after hovering over hyperlinks in the Description Panel.
Ensured that stop codons present in protein query strings are included in the search results.
Improved the import of multi-part qualifiers from Geneious.
Fixed an issue with undo of sequence color changes that are limited to a single strand.
Corrected the "Copy" shortcut when viewing a protein sequence or multi-protein alignment.
Ensured more robust behavior when adding primers to DNA sequences.
Turned on the display of truncated primer description data when full descriptions are toggled off in Primers view.
Corrected an issue in which simplified primer binding sites were not shown after modifying hybridization parameters.
Ensured that sufficient space is always allocated above displays of complex primer binding sites in Sequence view.
Turned on display of the parental enzyme set when viewing Nicking Endonucleases in Sequence and Map views.
Improved reliability when importing from Addgene.
Improved the import of Addgene sequences that contain slashes in their names.
Ensured that side toolbar buttons in dialogs are not hidden.
Corrected a regression in which two copies of common features such as EGFP were sometimes annotated when detecting common features.
Removed "Match Threshold" controls from the "Add to Common Features" dialog.

New in SnapGene 5.1.3 (May 22, 2020)

New in SnapGene 5.1.2 (May 11, 2020)

New in SnapGene 5.1.1 (May 7, 2020)

New Functionality:
Added an adjustable match threshold when detecting common features in new DNA files and in inserted DNA sequences.
(Suggested by Katherine Geromini)
Enhancements:
Provided the option of requiring up to 25 matching bases at the 3' end of a primer.
(Requested by Yield10 Bio)
Added a check for a 64-bit operating system before proceeding to install on Windows.
Made various textual enhancements.
Fixes:
Improved stability when deleting amino acids in protein sequences.
(Reported by Frank Fayang Zhou)
Enabled correct opening of double-clicked files with URL-encoded characters on Ubuntu Linux.
(Reported by Michael Jeltsch)
Enabled correct opening of sequence traces in collections on Windows and Linux.
(Reported by Frank Fayang Zhou)
Fixed a regression with copying selected regions in multiple sequence alignments.
(Reported by Leigh Harty)
Ensured reliable automatic trimming of low-quality ends of sequence traces.
(Reported by Jessica Saul)
Fixed a regression that could cause inappropriate headers to be shown in Features view after detecting common features.
Fixed a regression in which display options were not mirrored in sequences aligned with a reference DNA sequence.
Ensured that the "Confirmed experimentally" check mark is colored green.
Ensured proper display of the selection in a split Sequence view window after the selection is extended using the keyboard.
Improved stability when closing documents as well as exiting.
Prevented repeated appearance of a confirmation dialog when importing primers from a list into multiple files in a collection.
Ensured appearance of a warning message if no primers can be imported into multiple files in a collection.
Fixed an issue in which failing to import primers into files in a collection still marked those files as having unsaved changes.
Prevented inserted bases from being mistakenly shown in red when using the Edit DNA Ends dialog.
Fixed a regression that caused "Find" matches to be highlighted in green in Map view.
Configured the Select Range dialog that is invoked from a multiple alignment to auto-select the first range value, thereby allowing that value to be replaced quickly.
Corrected an issue in which the selection bar could report "aa" instead of "bases" for a selection in a DNA alignment.
Ensured that switching a pairwise alignment to a format that uses less vertical space never generates a blank window.
Corrected an issue in which the import of a primer that had been exported to GenBank format from Geneious might produce errors in the sequence and computed properties of the primer.

New in SnapGene 5.1.0 (Apr 15, 2020)

New in SnapGene 5.0.8 (Mar 24, 2020)

Enhancements
Added support for importing whole genome shotgun sequencing projects from NCBI.
(Requested by Chance Meers)
Added a sequence length indicator for sequences imported into the Assemble Contigs dialog.
Made various text, color, and icon enhancements.
Enabled "Save All", "Save to Collection", and "Save to Main Collection" commands when multiple files are selected in a collection.
Fixes
Corrected an issue that could cause the font used in Sequence view to be wrong on Windows.
(Reported by Ben Mcneil, Anna Doyle, Terese Tansey, and Dominic Esposito)
Fixed an issue that prevented double-clicking from opening files with spaces in their names on Lubuntu Linux.
(Reported by Sahand Jamal Rahi)
Ensured that features that wrap around the numerical origin are always properly displayed.
(Reported by Théo Grebert)
Corrected an issue that prevented opening sequence traces from remote locations when the file path includes non-Latin characters.
(Reported by Yusuke Maeda)
Fixed a stability issue when expanding the "Aligned Sequences" menu using SnapGene Viewer.
(Reported by Venkat Kalyana Sundaram)
Ensured correct creation of features with annotated gaps from selected aligned sequences.
(Reported by Olaf Kranse)
Ensured that newly imported sequences for aligning to a reference DNA sequence are always trimmed properly.
(Reported by Ridvan Cetin)
Prevented a collection from becoming unresponsive when adding files manually before dismissing the "Add DNA File" dialog.
(Reported by Gage Leighto)
Fixed an issue with writing feature names to GenBank format for assembly_gap, mobile_element, propeptide, regulatory, and telomere feature types.
(Reported by Hassan Tarabai)
Ensured that release notes are consistently shown when announcing that a new version of SnapGene is available.
Fixed an issue that resulted in the End User License Agreement dialog being too tall on smaller displays.
Ensured that matches to searches are always shown.
Ensured that Shift-clicking items in a list consistently results in a range-based selection.
Fixed an issue that prevented aligning a pair of DNA or protein sequences on some Linux systems.
Improved the conversion of DNA alignments to protein alignments.
Improved the mouse cursor for various controls that show tooltips but do not respond to mouse presses.
Ensured proper display of the message indicating that hybridization parameters need to be adjusted to show primer binding sites.
Removed the "Show alignments" button from the side toolbar in the Design Synthetic Construct dialog.
Ensured correct labeling of protein feature segments after making a protein from a DNA feature that contains introns.
Changed "bases" to to "residues" in the REFERENCE field when exporting protein sequences to GenPept format.
Corrected an issue with annotating common features that are found at the beginning of the sequence.
Improved highlighting of feature boundaries under the mouse cursor when using compact format in Sequence view.
Fixed an issue that prevented import of unsaved open sequences into the "Assemble Contigs" dialog.
Corrected a stability issue that resulted from closing a window while a menu was expanded.
Corrected an issue with aligning multiple DNA sequences that were recently imported from NCBI.
Ensured that header buttons are not always aligned with the column content when viewing a collection in List format.
Improved the behavior when double-clicking folders in collections.
Ensured that appropriate icons are shown next to unsaved files in the Window menu.
Fixed an issue that could prevent operation of the MUSCLE aligner.
Ensured that the Print and Save buttons in the toolbar are always correctly enabled or disabled when viewing a collection.
Corrected an issue in which protein sequences that count from a value other than 1 were sometimes shifted to the right in Sequence view.
Improved the display of a cursor placed within a gap when viewing alignments to a reference DNA sequence in Sequence view.
Corrected an issue that could result in feature labels being shown without being connected by a stem.

New in SnapGene 5.0.7 (Dec 17, 2019)

Enhancements:
Updated the common features database.
Added a "Clear List" action to the bottom of the menu in the "Import Primers from a List" dialog.
(Requested by Michael Baughn)
Fixes:
Fixed a regression with the background color for copied and exported gels.
(Reported by Russ Collins)
Improved compatibility of collections that are stored on a Google Shared Drive.
(Reported by Kurt De Vos and Michael Gotrik)
Improved stability when importing Vector NTI databases.
(Reported by Christoph Harms)
Corrected an issue that could cause aligned sequences to disappear after saving.
(Reported by Denise Lanza and Adrian R)
Substantially improved the decoding of alignment and sequence trace data from Vector NTI .cep files.
(Reported by Dale Cowley)
Fixed an issue in which aligned copied sequences were not always shown.
(Reported by Leonid V)
Corrected a regression that could result in inferior alignments to a reference sequence.
(Reported by Elisabeth Boger)
Restored the "Import Features from a SnapGene File..." command to the Features menu when working with a protein file.
(Reported by Anton Schmitz)
Improved the import of feature name, color, and directionality data as well as the map label from GenBank files exported by Vector NTI.
(Reported by Terete Borras)
Adding missing Edit → Copy Amino Acids menu actions when viewing a protein file in a collection.
Streamlined the interface by not displaying feature descriptions when detecting common features or importing features.
Ensured that tapping Enter correctly selects the contents of line edit fields in the Description Panel.
Ensured that ambiguous bases in traces are consistently shown as black on a yellow background.
Disabled Undo after making an edit to a very long DNA sequence because such operations cannot presently be undone.
Fixed a regression that caused deletions at the very beginning of a sequence to generate unexpected results and to be especially slow in large sequences.
Prevented adding a folder with a duplicate name in a collection by disabling the "OK" button instead of showing a scary window.
Improved the display of hybridization for primers in the Mutagenesis dialog and PCR-based cloning dialogs.
Enabled mutagenesis to be simulated using a primer that hybridizes perfectly but includes degenerate bases.
Made various format improvements for printing.
Ensured that ruler tick marks are always the correct height in Sequence view.
Improved colors for protein feature labels and lines with dark and other nonstandard background colors.
Ensured that all trace data are shown near trimming handles for aligned sequences.
Fixed a regression that sometimes resulted in disappearing features and grayed-out bases when nonaligned regions were shown by dragging the right trimming handle.
Added a warning before attempting to align pairs of very large sequences.
Fixed various visual issues when viewing nonaligned ends in an alignment to a reference DNA sequence.
Improved scrolling to mismatches and to the next or previous aligned region in an alignment to a reference DNA sequence, and properly disabled these controls when there is no destination for scrolling.
Fixed setting the collection folder icon when creating a new collection or while asking to open the main collection.
Corrected an issue that could cause the wrong name to be shown for unsaved open files when setting the options for a pairwise alignment.

New in SnapGene 5.0.6 (Nov 25, 2019)

New in SnapGene 4.2.5 (Sep 20, 2018)

New in SnapGene 4.2.4 (Aug 18, 2018)

Enhancements:
Increased the maximum allowed primer length to 250 bases.
(Requested by Eduardo Rodenas Martinez)
Dramatically sped up opening of large FASTQ files.
(Requested by Alfonso Valencia)
Enhanced the "Make Protein" converter to transfer DNA colors to the protein sequence.
(Requested by Luca Jovine)
Allowed protein_bind features to be bidirectional.
Provided the option, when using Folders view in a collection, to rename a selected file or folder by tapping Enter/Return on macOS or F2 on Windows.
Enabled import from NCBI of the reverse complement of a range of bases by specifying the right endpoint first.
Enhanced the multiple alignment tool to accept sequence traces as input.
Ensured that the Find bar and search results remain visible when switching to another sequence file in a collection and then back.
Updated the common features database.
Updated MAFFT from 7.312 to 7.407.
Made various color, textual, and other visual enhancements.
Fixes:
Improved network communication on Windows.
(Reported by F. Javier Piedrafita and others)
Fixed an issue where changing the name of a new DNA or protein file after pasting in a GenBank or GenPept sequence resulted in all features being lost.
(Reported by C. Dustin Rubinstein)
Fixed numerous issues with using proper group and decimal separators for European users.
(Reported by Thomas Reinard)
Improved the import of primers copied to the clipboard from programs such as Excel.
(Requested by Leah Tait and others)
Fixed an issue that resulted in content in the Description Panel not being visible or displaying the wrong font.
(Reported by Peter Nguyen, Pratyush Routray, and Cole Peters)
Improved the editing of custom common features.
(Reported by Shahar Bracha)
Improved stability when running SnapGene on a case-sensitive APFS file system.
(Reported by Jason Eads and Unekwu Yakubu)
Improved the decoding of features in Geneious files.
(Reported by Christine Eyler)
Prevented duplicate annotations that could occur when detecting common features.
(Reported by Wulf-Dirk Leuschner)
Prevented false positives when searching a collection by sequence name.
(Reported by Melissa Stokes)
Enabled the pasting into various controls of text that begins with "".
(Reported by Wulf Dirk Leuschner)
Modified the feature translation context menu to include a command for adjusting feature translation options rather than generic translation options.
(Reported by Chris Tipper)
Restored the NEB "2-Log DNA Ladder", which is identical to the newly renamed "1 kb Plus DNA Ladder".
(Requested by multiple confused scientists)
Improved stability when running Clustal Omega on some Windows installations.
(Reported by Yaseen Mamoori)
Corrected a regression that resulted in the font size being too large when printing.
(Reported by Tausif Alam and others)
Corrected a regression with copying from SnapGene and pasting into programs such as Excel.
(Reported by Leah Tait and others)
Ensured that the default directory for opening/saving/exporting is shown by default.
Improved the opening of RTF-encoded files.
Improved the warning system for shared licenses when the application has been idle for an extended period of time.
Prevented the selection (or selection bar) from being cleared inappropriately when editing a multiple alignment.
Improved stability when deleting residues within a multiple alignment.
Ensured that the selection bar is empty when a single row of gaps is selected in a multiple alignment.
Ensured that clicking the symbols button consistently pops up a dialog on Windows.
Prohibited renaming a folder in a collection to include a forbidden directory separator.
Fixed an issue with computing alignments with Clustal Omega, MUSCLE, and T-Coffee on Windows while logged in with a username that contains Unicode characters.
Ensured that when a DNA sequence is modified so that the number of feature segments drops to one, the remaining segment name is cleared.
Fixed an issue where -'s were shown when line breaking text in some places in the Japanese translation.
Improved the computation of sequence-profile alignments with MAFFT.
Fixed various issues with renaming a folder in a collection and then maintaining focus or retaining the selection.
Improved the behavior when using Find in Features view.
Ensured that features are consistently the appropriate height in circular maps.
Ensured that an amino acid name is displayed in Sequence view when a codon spans two adjacent translated features.
Improved stability when opening certain files.
Corrected the "Go To" dialog to show a blinking cursor instead of "1" when first opened.
Improved the behavior when creating or choosing a new Main Collection on Windows.
Fixed an isolated pliancy issue on macOS with Features and Primers views.
Corrected the behavior when Cmd/Ctrl-clicking feature names in Features view.
Ensured robust alignments with T-Coffee when the user account has spaces in the username.

New in SnapGene 4.2.3 (Jul 26, 2018)

New in SnapGene 4.2.2 (Jul 21, 2018)

New in SnapGene 4.2.1 (Jul 13, 2018)

New in SnapGene 4.2 (Jul 11, 2018)

New in SnapGene 4.1.9 (Apr 24, 2018)

New in SnapGene 4.1.8 (Apr 24, 2018)

New in SnapGene 4.1.7 (Mar 12, 2018)

New in SnapGene 4.1.6 (Feb 26, 2018)

New Functionality:
Added the ability to press Alt/Opt while mousing over a sequence trace to see all four peak heights.
(Requested by Teisha Rowland)
Provided additional TaKaRa DNA markers.
(Requested by fky19842004)
Enhancements:
Enabled bidirectional sorting of a collection by Code Number, Date Added, or Date Created by clicking the column buttons.
Made horizontal scrolling easier to discover by setting ∞ as the default fixed line width.
Fixes:
Fixed an issue on Windows where automatically launching the application after running the installer resulted in the settings being stored in the wrong location and administrator file ownership and permissions being used when saving.
(Reported by Clay Fuqua)
Improved the output when exporting and printing agarose gels, especially while using high-DPI displays.
Corrected an erroneous message that was shown when exporting common features.
(Reported by Edward Wallace)
Ensured that gray sequence colors are visible after saving and re-opening a file.
(Reported by Genevieve Tauxe)
Fixed a regression to ensure that gaps in aligned sequences are always visibly represented.
(Reported by Dustin Rubinstein)
Enhanced the importer for CLC Bio files.
(Reported by Rabea Wagner)
Fixed an issue with opening certain DNA Strider files.
(Reported by Michael Nassal)
Improved the import of primers from SeqBuilder files.
(Reported by Lakxmi Subramanian)
Ensured that error messages in the primer dialogs are completely visible.
Enhanced the flexibility of controls for adding and importing primers copied to the clipboard.
(Requested by Seth Goldman)
Prevented a slowdown and potential data omission that could occur when using the same open file for multiple inserts in a manipulation dialog.
(Reported by Seth Goldman)
Ensured that modifications to open documents are reflected in manipulation dialogs that already have those documents loaded.
Prevented duplicate forward slashes from getting into the recent collections list.
Improved the default location for saving sequences in an imported archive.
Prevented unwanted data from being retrieved from an imported sequence record when including extra features added by NCBI.
Blocked accidental toggling of the "File Name" column in a collection list.

New in SnapGene 4.1.5 (Feb 6, 2018)

Enhancements:
Preserved history colors for the selected operation when printing History view.
(Requested by Edward Wallace)
Enhanced placeholder files to support custom map labels and aliases.
Added WATSON MW Markers.
(Requested by Rui Tada)
Added Genessee Scientific MW Markers.
(Requested by Aaron Miller)
Added G-Biosciences MW Markers.
Fixes:
Ensured that bottom strand features are always imported from NCBI.
(Reported by Christiane Widmann)
Removed inappropriate quotes when exporting /number qualifier values to GenBank format.
(Requested by Simon Zumkeller)
Updated restriction enzyme website URLs for New England Biolabs HF enzymes and Promega enzymes.
Enhanced opening of GenBank files to omit placeholder values (".") in references.
Ensured that "Direct Submission / Exported by SnapGene" references are ignored when importing from text formats.
Fixed an issue with opening some Geneious files.
Improved the retention and updating of code numbers when adding sequences to a collection.
Corrected the display of mismatches and aligned bases for certain reverse aligned sequences.
(Reported by Leonid)
Fixed a regression with modifying the Description or Collection Author in a collection.
Enhanced the collection List view to support Page Up, Page Down, Home, and End keys.
Ensured that the collection toolbar navigation Back/Forward buttons autoscroll in List and Folder views.
Improved stability when closing a collection.
Added a clean-up step in the collection interface when rendering the Description and Comments fields after switching between sequences.
Ensured that the font size setting is respected when printing History view.
(Reported by Edward Wallace)
Improved the consistency of displaying primer Tm and length for the primer controls in various manipulation dialogs.
Corrected an issue where changing the name of the Product in the Overlap Extension PCR dialog did not update the name as shown in Map view.
Prevented the occasional display of a "Sorry, could not create collection." message when a collection actually was created.
Improved the behavior of the importer for certain GCK files.
(Reported by Tiffany Su)

New in SnapGene 4.1.4 (Jan 11, 2018)

New in SnapGene 4.1.3 (Dec 23, 2017)

New in SnapGene 4.1.2 (Dec 6, 2017)

New in SnapGene 4.1.1 (Dec 4, 2017)

New in SnapGene 4.1.0 (Nov 8, 2017)

New Functionality:
Enhanced collections to support a folder view of the files.
Added support for formatting and updating code numbers for sequences stored in collections.
Provided the option of marking sequences in a collection as part of a "Working Set" that can be easily viewed and manipulated.
Added the ability to drag files from a collection in order to (a) copy them to another location or collection, (b) move them to the Trash, or (c) attach them to an email message.
Added an undoable "Trim History Tree" command to the pull-down menu at the top right of History view.
Added a "Batch Trim File Histories" command to the File menu.
(Requested by Dan Piraner)
Added a new preference for automatically trimming the history of a sequence.
(Suggested by Dan Piraner)
Added the ability to choose enzymes that are palindromic, uninterrupted
(no internal N's), or nondegenerate (A, C, G, and T only) to the Choose Enzymes dialog.
(Requested by Vadim Timerbaev)
Added the option to import only primers that have a unique binding site.
(Requested by an anonymous customer)
Added absorbance values to the Properties tab for protein sequence files.
(Requested by Genevieve Labbe)
Added an "Import from Another File" button to the "Edit References" dialog.
(Suggested by Karl Brune)
Added "Date Created" as a sortable field when viewing a collection.
(Requested by Seth Goldman)
Enabled drag and drop of entire folders into a collection, and added an "Import Folders into Collection" command.
Added a context menu to the Browse Common Features dialog's list to enable editing or removing a feature, adding or removing a feature from the Favorites list, or opening a feature in a new window.
Added a "Duplicate in New Window" button to the Browse Common Features dialog.
Added the ability to order constructs directly from Synbio Technologies.
Enhancements:
Added support for multiple copies of the following qualifiers: allele, cell_line, cell_type, citation, clone, clone_lib, cultivar, dev_stage, experiment, function, host, isolate, lab_host, map, note, operon, PCR_conditions, phenotype, pop_variant, product, standard_name, strain, sub_clone, sub_strain, tissue_lib, tissue_type.
(Requested by Novozymes)
Added an option in Preferences for hiding the dashed line tick marks in sequence traces.
(Requested by Raffaele Fiorenza)
Reduced the minimum primer length for simulating mutagenesis.
(Requested by Sriram Vijayraghavan)
Improved the import of multiple files of varying types into a collection.
(Requested by Dan Kraut)
Added history colors for "Splice to Remove Introns".
Enhanced History view to display annealed oligo names.
Enhanced the Addgene importer so that when only a partial sequence is available, the topology is shown as linear, unless the backbone size is available, in which case a circular sequence padded with N's is shown.
Added the option of either preserving or updating the Date Added attribute when a file in collection is replaced by importing a new copy.
Ensured that after a common feature is edited, the list scrolls to show the edited feature if its name was modified.
Added "Swiss-Prot" to the list of formats offered when using Batch Convert File Format.
Made flipping a sequence trace an undoable action.
Added the option of requiring an exact match when replacing a feature name, primer name, or sequence author for sequences in a collection.
Added "Find Protein Sequence" and "Find Enzyme / Feature / Primer" commands to the Edit menu, by creating a cascading "Find" menu that improves discoverability.
Removed the compact format button from the side toolbar in the Anneal Oligos dialog because it provided minimal utility.
Added a warning to help prevent accidental pasting of a copied DNA sequence into the protein search controls.
Enhanced the Edit Feature dialog so that when using "Create Feature Segment", the list scrolls if necessary to make the created segment visible.
Added support for "Make Protein" from within the Browse Common Features dialog.
Added an alert when using a file with over 25 levels of ancestors, to indicate that simulations may be slow unless the history is trimmed.
Added a draggable splitter to the DNA feature dialogs to allow more space to view qualifier or segment information.
Added support for "New File From Selection" to the Simulate Agarose Gel dialog.
Made various optimizations.
Enhanced the color, alignment, and look and feel of buttons and other interface elements.
Reduced Linux download size.
Fixes:
Enhanced the GenBank importer to make better use of the SOURCE field.
(Requested by Novozymes)
Enabled the import of malformed GenBank files that lack a LOCUS line.
(Reported by Yoshihisa Oda)
Enhanced the reliability of the DNASTAR SeqBuilder and EditSeq importers.
(Reported by Kensuke Kataoka and Alex Justen)
Improved the reliability of recognizing the default genetic code when opening DNASTAR SeqBuilder files.
(Reported by Kensuke Kataoka)
Fixed an issue that prevented import of some Geneious files.
(Reported by Karl)
Fixed an issue with decoding GenBank files saved by ApE where N's were encoded as *'s.
(Reported by Bianca Nijmeijer)
Fixed an issue where remote recent files were sometimes not listed after quitting and starting the program.
(Reported by Dr Fanny Passot)
Fixed an issue with importing some records from NCBI.
(Reported by Thomas Folliard)
Improved the reliability of Undo/Redo after saving.
(Reported by Leonid Valentovich)
Enabled the Copy command in the Save/Save As dialogs, while disabling other irrelevant menu commands.
(Reported by David Scalzo)
Enabled use of the Copy keyboard shortcut from within the DNA feature dialogs.
(Reported by Juan Antonio Raygoza Garay)
Fixed an issue with importing some sequences from Addgene.
(Reported by Alexandra Iouranova)
Ensured that Sassafras-based installations will not consume a second license if a second copy of SnapGene is launched on the same computer.
Improved feature selection behavior so that when two overlapping features are selected, the union of the two feature sequences is selected.
Fixed the following unreliable shortcuts in cascading menus on macOS: File → Import → NCBI Sequence (Cmd+Shift+O) Edit → Copy Bottom Strand → 5'to 3' (Cmd+Shift+C) Edit → Find → [Various] View → Toolbars → Toggle [Top | Side] Toolbar All Commercial (Cmd+Shift+Opt+A) Nonredundant Commercial (Cmd+Opt+A) Unique Cutters (Cmd+Opt+1) Unique & Dual Cutters (Cmd+Opt+2) 6+ Cuters (Cmd+Opt+6) Unique 6+ Cutters (Cmd+Opt+7) Actions → Restriction Cloning → Insert One (Cmd+Opt+I) Actions → OE PCR → Overlap Two (Cmd+Shift+D) Tools → Align → Various
Fixed a number of memory leaks.
Made various stability improvements.
Fixed an issue where the "Save Changes" button was not always enabled when one or more files was selected while viewing "Unsaved" files.
Fixed an issue where history view did not clear when multiple files in a collection were selected.
Improved the process of assigning files imported into a collection to the correct area of the collection.
Fixed an issue with sorting collection files by date.
Fixed the macOS shortcut (Cmd+Backspace) discarding unsaved changes in Collections.
Fixed the macOS shortcut (Cmd+Backspace) closing a document without updating.
Edit → Select All and Edit → Invert Selection can now be used to select files in collections.
Ensured that feature directionality is preserved when exporting to GenBank format and re-importing.
Enabled the import of large Geneious files.
Disabled menu commands that should not be available in manipulation dialogs.
Removed nonfunctional SCF / ZTR / FASTQ options from the Batch Convert File Format dialog.
Fixed an issue where Edit → Find Protein Sequence could sometimes show the "Find Feature" controls instead while viewing a protein sequence.
Prevented a blue line from appearing inappropriately when clicking on the upper ruler in Sequence view.
Enabled the launch dialog to be closed on macOS even when it is configured to appear when all windows have been closed.
Modified the window announcing a new SnapGene version so that it no longer requires an immediate decision about updating.
Ensured that "Show Selected Features" and "Hide Selected Features" are properly enabled when interacting with protein sequences.
Fixed an issue where when importing multiple files into a collection, files could sometimes be shown in the wrong category.

New in SnapGene 4.0.8 (Nov 4, 2017)

New in SnapGene 4.0.7 (Oct 21, 2017)

New in SnapGene 4.0.6 (Oct 10, 2017)

New in SnapGene 4.0.5 (Sep 16, 2017)

New in SnapGene 4.0.4 (Sep 2, 2017)

New in SnapGene 4.0.3 (Sep 2, 2017)

New Functionality:
Added Thermo Fisher O'GeneRuler MW markers.
(Requested by Alexandra Iouranova)
Added TransGen Biotech MW markers.
(Requested by Xiong Qin)
Enhancements:
Added "TransGen Biotech" to the Sequence Author list.
Added support for "citation" and "PCR_primers" qualifiers.
Added support for the "/note" qualifier for J_segment features.
Improved the naming of imported features.
Fixes:
Ensured that code numbers and aliases are always shown in a collection list.
(Reported by Alina Goldstein)
Removed an outdated message about AgeI losing activity 37°C.
(Reported by Georg)
Fixed an issue where the keyboard shortcut for "Choose Enzymes" stopped working on Windows.
(Reported by Chris Jacobs and Fabian Bietz)
Improved loading performance of Recent File lists for network mapped drives.
(Reported by Maarten Rotman)
Configured the importer to open files written by CLC Bio 6.9 and prior.
(Reported by Dan Moran)
Enhanced the GenBank importer to convert a nonstandard qualifier to a /note qualifier that preserves the original qualifier name as a prefix.
(Requested by Novozymes)
Allowed iDNA and misc_difference features to be forward and reverse directional.
(Requested by Novozymes)
Fixed an issue when exporting feature names to GenBank/GenPept/EMBL/SwissProt format.
(Reported by Novozymes)
Ensured reliable import and export of strings enclosed in quotes in GenBank qualifiers.
(Reported by Novozymes)
Improved the reliability of importing and exporting GenBank feature names as well as deprecated and nonstandard feature types.
(Reported by Novozymes)
Fixed an issue where the wrong number of annealed bases could be displayed in the selection bar for a primer that has multiple binding sites.
(Reported by Chu Chen)
Enhanced how nonstandard feature types are migrated to /label qualifiers.
(Suggested by Novozymes)
Fixed an issue that could result in an enzyme being listed multiple times for a given restriction site or in the Choose Enzymes dialog.
(Reported by Nicola Zilio)
Improved the accuracy of extending selections by Shift-clicking while viewing an alignment.
(Reported by Leonid Valentovich)
Ensured that /note qualifiers are retained when decoding feature names from imported files.
(Requested by Novozymes)
Prevented the "File" and "Edit" menus from being shown behind other controls when using the Add/Edit/Duplicate Feature dialogs with a protein sequence.
(Reported by Icon Genetics)
Ensured that the selected file in a collection window is listed as an open file in Action window source menus.
Improved the responses of the collection window Replace controls.
Updated the collection window behavior so that after importing files, the display switches automatically to the “All” setting.
Ensured that keyboard shortcuts for switching enzyme sets work consistently while viewing a collection.
Prevented outdated messages from being shown after installing a software update.
Ensured that a linear map remains visible in Map view after exporting the map image.
Fixed an issue with displaying a map alias when exporting to a raster format.
Improved the margins for printed output.
Adjusted the Recent File menu tooltip position on Windows and Linux.
Improved the positioning of context menus in the collection window list.
Enhanced the GenBank importer to include a backslash (“/“) before a nonstandard qualifier during conversion to a /note qualifier.
Ensured that imported nonstandard or forbidden qualifiers are visible in a /note qualifier within the Add/Edit Feature dialogs.
Prevented the appearance of lingering phantom menus on macOS.
Ensured that if multiple suitable GenBank qualifiers are available for naming an imported feature, the first such qualifier is used.
Improved the import of partial sequences from Addgene.
Prevented the appearance of inappropriate transient messages while changing the list selection in a collection window.
Fixed an issue that prevented Action commands from working when no file was selected in an open collection window.
Prevented descents of characters from being clipped in various search fields.
Fixed the plain file icons in Recent Files menus on Linux.

New in SnapGene 4.0.2 (Jul 28, 2017)

New in SnapGene 4.0.0 (Jul 25, 2017)

New Functionality:
Added support for browsable “collections” that can be used to organize and sort DNA and protein files as well as miscellaneous files.
(Requested by dozens of customers)
Provided the option of defining a Main Collection that is accessible with dedicated commands.
Enabled rapid searching of collections by multiple criteria.
Enabled batch replacement within collections of DNA and protein sequences, feature and primer names, and sequence authors.
Added import and export options for protein sequences in Swiss-Prot format.
(Requested by Novozymes)
Added "Annotate Lowercase Regions as Introns" command.
(Requested by Helena Pires)
Added "Convert Introns to Lowercase" command.
Added support for sequence-free placeholder files.
Added optional “aliases” for display of alternative sequence names in Map view and in collection lists.
Enabled SnapGene to show dynamic alerts and other targeted messages.
Enhancements:
Enhanced sequence trace windows to support Edit → Make Uppercase/Lowercase.
Configured the Add Feature dialog so that mandatory qualifiers that have not yet been specified are shown by default.
(Suggested by John Ticehurst & Brendan)
Improved the GenBank and EMBL file format exporters to include primer data.
(Requested by Novozymes)
Allowed the preferences file to disable checking for and installing updates by setting "updates/disable=true".
(Requested by Novozymes)
Added a Cmd+Shift+K keyboard shortcut for "Set DNA/Protein Color”.
(Requested by Chandler)
Made various optimizations and textual and color enhancements.
Added Aldevron to the list of standard authors.
Added "Peak Height: #" information to trace viewer tooltips, and removed quality information from tooltips for failed called bases (N's).
Added the ability to override the Flexera server address and port number encoded within a license file, to facilitate moving a Flexera server or using multiple Flexera servers on disparate networks.
Updated and improved the Addgene plasmid importer.
Enhanced the feature dialogs regarding qualifiers that support multiple values, to support clearing a single qualifier value by clicking the minus button.
Enabled rapid insertion of a feature with the Insert Feature dialog by double-clicking within the list.
Added File and Actions menus to the launch dialog on Windows, so that the researcher can create a synthetic construct or plan a cloning experiment without first opening a file.
Enhanced manipulation dialogs so that the viewer contents are blurred before a template is specified, making it easier to read a message shown on top.
Added the option during logging off or shutting down of saving documents, discarding changes, or canceling the logout/shutdown.
Improved file associations and icons on Linux.
Optimized the import of primers from a list.
Improved reading and writing GenBank files, and prioritized use of the /label qualifier for storing feature names.
Updated the common features database.
Enhanced importing references from EMBL to use RG entries if no RA entries are provided.
Added biotechrabbit MW markers.
(Requested by Nadine Waeber)
Added Penn State MW markers.
Fixes:
Prevented an error message from being shown twice when attempting to edit a primer by double-clicking it within a manipulation dialog.
(Reported by Walter Bonacci)
Fixed various issues with feature and primer tooltips, and with exporting feature and primer qualifiers to GenBank and EMBL formats.
(Reported by Xavier Danthinne)
Improved the rendering of arrowheads for reverse directional ORFs that wrap around the numerical origin in linear maps.
(Reported by Max Juchheim)
Ensured that "Linearize by PCR" is automatically checked in a manipulation dialog after replacing an enzyme-based selection with a standard selection.
(Reported by John Murray)
Enabled the opening of older Geneious files.
(Reported by Sandra Malmgren Hill)
Restored consistent opening of .exdna files created by EnzymeX.
(Reported by Yuichiro Tsuchiya)
Fixed an issue that prevented "Open" links on web pages from working with SnapGene Viewer (and in some cases SnapGene) on Windows if the application was not already running.
(Reported by Henry Chu)
Fixed an issue where on NTFS volumes all files were falsely assumed to be readable and writable.
Ensured comma separation of large size values when exporting features.
Included "About SnapGene" as an entry that can appear in the list of open windows on macOS.
Ensured that minimizing or restoring a sequence trace results in an associated Chromatogram Data dialog being hidden/restored.
Improved the name in the Windows menu for an Align Full Sequence window.
Corrected a cosmetic issue when using the Replace Bases dialog for a sequence trace when no replacement was specified.
Prevented an entire sequence or trace from being deleted.
Ensured that Edit → Paste Reverse Complement pastes the reverse complement instead of the copied text when interacting with a sequence trace.
Enabled updates to local enzyme sets to be reflected in open manipulation dialogs.
Enabled Edit → Undo/Redo and the associated keyboard shortcuts to work while using the Insert Codons dialog.
Corrected a warning message about deleting the underlying sequence to specify “protein” rather than “DNA” when working with a protein sequence file.
Corrected a command in the Edit menu to read “Delete Primers” rather than “Delete Bases” if a pair of complementary primers is selected.
Corrected a menu command to read “Amino Acids” rather than “Bases” when working with a protein sequence file.
Fixed an issue in which selecting one or more primers that do not result in a DNA selection, and then holding Opt while clicking Edit → Delete Primers, would inappropriately generate a request for a DNA selection.
Ensured that "Zoom All" does not attempt to zoom windows that lack support for maximizing.
Enabled the "Zoom" and "Enter Full Screen" commands for all windows that support full screen mode.
Prevented the Restriction Enzymes window from allocating its own menu bar on macOS.
Ensured that the file extension for open sequence trace files is listed in the Window and Dock menus.
Prevented the "Set DNA Color" command from being enabled in read-only contexts such as manipulation dialogs where such changes would be lost.
Fixed an issue where View → Toolbars → Show/Hide Toolbar could not be used to toggle the side toolbar in manipulation dialogs.
Enabled showing/hiding and customizing a top toolbar in the New Synthetic Construct dialog.
Prevented recent files from being cleared if SnapGene is run from the command line with an option that exits the app before the Recent Files list has loaded.
Improved the behavior with code signing dll's and exe's on Windows.
Improved the default folder name when exporting two or more common features.
Improved the error message shown when attempting to register a network license from an invalid IP address.
Corrected the font size for aligned sequence names at the lower left of Sequence view on Windows.
Hid the scaling slider when showing an aligned sequence of a type such as FASTQ that has quality data but no trace data.
Improved the rendering of protein feature lengths when printing Features view.
Fixed an issue with the default Start folder name when installing on Windows.
Ensured that menu tooltips are invisible when a parent cascading menu is hidden.
Adjusted the Sequence Author combobox in the Description Panel to not display a clicked action text such as "Edit Sequence Author List...".
Ensured that undoing changes to fields in the Description Panel can be achieved by invoking the Undo action once rather than twice.
Corrected the algorithm for choosing a directory during repeated export of common features.
Prevented the side toolbar from being compressed when a window is resized.
Improved the automatic design of primers for Gateway fragments that are being inserted in the reverse orientation.
Corrected the display in Sequence view of selected segments of reverse directional features with run-on translations.
Prevented certain amino acids from being duplicated in the amino acid pull-down menu for the /transl_except qualifier in the feature dialogs.
Improved import and export of the /transl_except qualifier from other formats such as GenBank.
Ensured that if a mandatory qualifier remains to be specified, a different qualifier can be edited within the feature dialogs.
Improved the display of pliancy when mousing over the sequence name in a linear map.
Fixed an issue with the file icon and path when right clicking the title bar for a sequence trace on macOS.
Prevented an empty ruler from appearing in Sequence view of a cloning dialog when no template is loaded.
Ensured that DNA colors for top and bottom strands are exchanged when inserting a fragment in the reverse orientation.
Fixed various issues with viewing long sequence traces.
Made various stability improvements.
Prevented full sequence /source features from being exported when using the EMBL format to save or export DNA sequences.
Ensured that *'s in protein files can be imported.
Fixed an issue with writing the last base # per line when exporting DNA files to the EMBL format.
Ensured that the Browse Common Features and Insert Feature dialogs list the correct feature subset when the dialog is opened repeatedly.

New in SnapGene 3.3.4 (Apr 28, 2017)

New in SnapGene 3.3.3 (Feb 10, 2017)

New in SnapGene 3.3.2 (Feb 2, 2017)

Enhancements:
Enabled the “Import from Addgene” command to support searching by plasmid number.
Added "propeptide" to the list of allowable feature types.
Fixes:
Fixed a visual issue where a portion of Features or Primers view could be displayed outside the scrolled region.
(Reported by Cor Breukel)
Restored the proper response with pinch to zoom on macOS.
(Reported by Yuta Chigi)
Improved the import of GenBank files containin empty LOCUS lines.
(Reported by Guangyong Ma)
Ensured that the Restriction Enzymes and Enzyme Database dialogs can be shown repeatedly.
(Reported by Scott James)
Enhanced the stability of the importer for ApE feature libraries.
(Reported by Jeremy Rabinowitz)
Fixed an issue that prevented portions of some primers from being shown as hybridizing to the template.
(Reported by Elena Fujiwara)
Improved the import of GenBank files containing nonstandard feature types and qualifiers.
(Requested by Reinhard Wilting)
Restored the original behavior for the Select Range command when no selection is already present.
Enabled the creation of nondirectional mat_peptide, sig_peptide, and transit_peptide features as well as reverse directional S_region features.
Fixed an issue where protein searches might not return matches when ORFs were allowed to begin at an end of a linear sequence.
Improved how ORFs are shown when they are allowed to start at an end of a linear sequence.
Improved alignment of controls in the Add/Edit/Duplicate Primer dialogs.
Enhanced the "Import from NCBI" dialog to tolerate … as well as .. when specifying a base range.
Changed the update notifications so that if your copy of SnapGene is out of date, detailed information is shown about the latest point release but not any subsequent bug fix release.
Configured the updater so that if you choose to skip a release, SnapGene no longer reminds you about any associated bug fix releases.
Fixed various issues that caused the alignment display to scroll when toggling the visibility of aligned sequences.
Improved history recording so that endpoint stickiness is properly stored for ancestral sequences even if changes made using “Edit DNA Ends” were not saved before a cloning simulation.
Fixed an issue where uninstalling on Windows did not remove all installed dll's.
Improved the appearance of SnapGene on a standard-DPI external display paired with a high-DPI primary display on Windows.
Improved the import of multiple /note qualifiers from GenBank files.

New in SnapGene 3.3.1 (Jan 6, 2017)

New in SnapGene 3.3.0 (Dec 22, 2016)

New in SnapGene 3.2.1 (Aug 23, 2016)

New in SnapGene 3.2.0 (Aug 9, 2016)

New Functionality:
Codon usage tables.
Choose Alternative Codons capability.
Back translation from protein to DNA.
Import Addgene Plasmid capability.
Import SnapGene Online Sequence capability.
Importer for CLC Bio files.
(Requested by Anders Aspberg, Zhe Yan, and Seth Goldman)
Importer for FASTQ files.
Ability to align FASTA archives as well as FASTQ files and archives.
(Requested by Patrick Connelly and Tyler Bradshaw)
Ability to save sequence traces to FASTQ format.
Degenerate codons in the menus for the Primer dialogs (Insertions tab).
Import of oligos from Vector NTI® databases.
Import of Vector NTI® oligo archives.
(Requested by Anton Ivankin)
Import of Clone Manager primer collection files.
Ability to show/hide features or primers inside the selection.
(Requested by Michael at Novozymes)
Command line interface for converting files.
(Requested by Willem-Jan Waterreus)
Support for automatically saving and exiting after a user-defined inactivity period if using a shared license.
Enhancements:
Added shortcut for Invert Selection (Cmd+Shift+I; the new shortcut for Insert Fragment is Cmd+Opt+I).
(Requested by Amin Mahpour)
Enabled files to be dragged and dropped onto the gel image or fragment list in the Simulate Agarose Gel dialog.
(Requested by Alejandro Serrion)
Enabled export of Map or History view to rasterized formats such as PNG without the "Created by SnapGene®" watermark.
(Requested by Andrew Flies)
Added MIDSCI ladders.
(Requested by Derek Englert)
Enhanced Select All, Select Range, and Go To for navigating and selecting aligned sequences.
Enhanced Make Protein and Export Selected Protein for use with protein selections in aligned sequences.
Enabled imported NCBI sequences to be either viewed directly or saved to disk.
Sped up the removal (and undoing the removal) of a large number of aligned sequences.
Added a Clear button to various search controls.
Updated the enzyme database to indicate additional enzymes that require multiple sites for efficient cleavage.
Added a ”Request Free Trial" button to the Registration dialog.
Improved the look and feel of rounded ovals on low DPI displays.
Made various color, icon, textual, and other interface enhancements.
Enhanced Anonymous Statistics to send both the default locale and the user’s preferred locale.
Fixes:
Fixed an issue where after resurrecting some very old sequences you could be forced to save when closing if SnapGene was configured to update older files automatically.
(Reported by András Tálas)
Improved the display of long alignments that wrap around the numerical origin.
(Reported by Leonid Valentovich)
Improved the consistency of primer Tm calculations in various parts of the interface.
(Reported by Dan Lysko)
Enhanced the map exporter to encode the correct resolution within the exported file.
(Reported by Alan Myers)
Fixed an issue when working with shared files on Windows.
Fixed an issue where after importing enzyme sets using the Manage Enzyme Sets dialog, the recent directory was not re-used during a subsequent import.
Ensured that "Translation Options..." is omitted from context menus if generic translations/ORFs are toggled off.
Ensured that the "Set Enzyme Preferences..." action in the side toolbar menu is consistently disabled in modal dialogs.
Improved the painting of primer outlines in an alignment when the most 3' base of a primer abuts a gap.
Ensured correct processing of FASTA files that contain carriage returns but not newline characters.
Added a pair of sanity checks to avoid moving invalid files (lacking static content such as the nucleotide sequence) into place when performing a Save or Save As operation.
Fixed an issue in the Add/Edit Feature dialogs where if a yellow message was shown for a reason other than a nonstandard genetic code, clicking this message would show the Translation Options dialog even if the feature was not translated.
Fixed an issue with showing the paid feature preview dialog from a modal context.
Ensured that enzymes and primers outside the zoomed range are not included when printing a linear map.
(Reported by Fanny Passot)
Ensured that the correct portion of an ancestor is shown in History view after using an entire sequence with Make File from Selection or after using Make Protein with a full sequence feature.
Improved the display of the used and unused portions of a linear protein sequence in History view.
Improved primer tooltips to not allocate extra space above a primer description.
Prevented Find matches from being highlighted in the scroll bar when scrolling is unnecessary.
Fixed "Import Vector NTI® Database" on OS X to look for a database under "/Library/Application Support/VNTI Database".
Added missing import actions to the launch dialog and Dock menu on OS X.
Ensured that colors and uracil positions are preserved when updating older files.
Improved the display of features in aligned sequences when insertions or deletions wrap around the numerical origin.
Fixed an issue where the enzyme controls in the Anneal Oligos dialog offered "Start" and "End options for adding enzyme sites.

New in SnapGene 3.1.4 (May 18, 2016)

New in SnapGene 3.1.3 (May 16, 2016)

New in SnapGene 3.1.2 (Mar 25, 2016)

New in SnapGene 3.1.1 (Mar 17, 2016)

New in SnapGene 3.1.0 (Mar 9, 2016)

New Functionality:
A compact Sequence view mode.
Option to display features on the DNA map line.
Support for NEBuilder HiFi DNA Assembly.
Ability to regenerate individual restriction sites in the vector when designing primers for Gibson Assembly and In-Fusion cloning.
Importer for DS Gene files.
Importer for GeneTool files.
Enhancements:
Enabled Gibson Assembly of linear fragments to generate a circular product.
Added Lucigen DNA ladders.
Added pcDNA3.2/capTEV-NT/V5-DEST and pcDNA3.2/capTEV-CT/V5-DEST Gateway Destination vectors.
Ensured that SnapGene is offered as an option in the "Open With" context menu on Windows.
Added a draggable splitter to the list in the Browse Common Features dialog.
Added a check box to the Browse Common Features dialog to make it easier to enable detecting a translated feature by its protein sequence.
Added a keyboard shortcut for "Copy Protein”.
Configured the "Set DNA/Protein Color" dialogs to remember the most recently used color and strands.
Added a check so that if a newly created feature will not be shown in the circular map without prioritization, SnapGene offers to prioritize it.
Improved how multiple adjacent copies of the same feature are labeled in maps.
Ensured that if enzymes and primers (DNA) or regions (Protein) are toggled off, the locations/numbers button in the side toolbar is disabled.
Added a "Trim Selected Region" command to the context menu when right clicking aligned sequences in Sequence view.
Added the Cmd+Backspace shortcut on OS X for discarding unsaved changes.
Added "lncRNA" and "ribozyme" to the list of predefined /ncRNA_class qualifier values.
Added "Gen9" to the list of sequence authors.
Sped up scrolling in Sequence view while the minimap is visible.
Sped up loading and displaying circular maps in action dialogs.
Enhanced the Import from GenBank dialog to support importing the antisense strand by using the "complement" keyword.
Implemented various color, textual, and alignment enhancements and other optimizations.
Fixes:
Removed a duplicate "Enter/Exit Full Screen" command from the View menu on OS X 10.11.
Fixed an unlikely issue that could result in truncating some Jellyfish, Visual Cloning, and DNADynamo files.
Fixed an issue where custom primers for PCR were not migrated to the amplified product if their names were edited by copying and pasting.
Enabled the detection of attB1.1 and attB2.1 Gateway cloning sites.
Ensured that newly saved files use default attributes for the directory in which they are saved on Windows.
Improved the display for a reverse directional primer with a 5' tail extending beyond the end of the sequence when using horizontal scrolling.
Fixed an issue where the wrong tab was sometimes shown when clicking a link to pull up the relevant setting in the Preferences dialog.
Improved the agarose gel display when using a Japanese translation.
Enabled the import of protein sequences with accession numbers for PDB structures.
Enhanced the EMBL file importer to recognize files exported from Vector NTI.
Fixed an issue with displaying enzyme, feature, and primer labels on the right side of some circular maps.
Fixed an issue where the number of mismatches in an alignment was sometimes printed incorrectly.
Fixed issues with exporting dates in EMBL/GenBank format.
Prevented invalid characters from being included before sequence data when opening EMBL or GenBank files that include a comment on the ORIGIN line.
Improved decoding of the code number when opening EMBL files.
Enhanced the GenBank importer to tolerate "pb" as the unit length in the LOCUS line.
Enhanced the GenBank importer to ignore empty fields marked with the “/“ character.
Embedded application information and a manifest for Windows, and code signed all .exe and .dll files.
Configured the label controls in the side toolbar and Map & Sequence Options dialog to be disabled if features/regions are toggled off.
Fixed an issue where the DNA tab of the Preferences dialog would not list newly saved custom enzyme sets while the dialog was open.
Fixed an issue that could result in a hang.
Removed Pyl, Sec, and Xle from the “Insert Codon” controls in the Add/Edit Primer dialogs, and added TAA (Ochre), TAG (Amber), and TGA (Opal) to the list of possible codons when inserting Xaa.
Fixed issues with showing the genetic code in the Add/Edit Feature dialogs and Features view when Ochre, Amber, or Opal were used.
Improved feature and ORF tooltip placement when the tooltip could not be shown in the preferred location outside a circular map.
Ensured that regions of overlap are properly highlighted in black in History view for fragments that are flipped while performing Gibson Assembly or In-Fusion cloning.
Ensured that after simulating Gibson Assembly or In-Fusion cloning, portions of fragments or the vector that were trimmed away are highlighted in white in History view.
Fixed issues with opening DNADynamo and Jellyfish protein files.
Improved the display of certain feature labels above a linear map.
Fixed an issue that prevented software update from working for SnapGene Viewer on Mac OS X. -Fixed an issue with detecting "misc_RNA" and other feature types for which a single nucleotide can be omitted from either end.
Fixed an issue where "Nonstandard genetic code" was unnecessarily displayed in the "Edit Feature" dialog after making a feature from an aligned sequence.

New in SnapGene 3.0.3 (Jan 12, 2016)

New in SnapGene 3.0.2 (Jan 3, 2016)

New in SnapGene 3.0.1 (Dec 21, 2015)

New in SnapGene 3.0 (Dec 21, 2015)

New Functionality:
Support for standalone protein sequence files, including conversion from translated DNA features to protein sequences. SnapGene can now open the following protein file formats: DNADynamo, DNASTAR (EditSeq, SeqBuilder) DNA Strider FASTA, GenBank/GenPept MacVector Vector NTI (pa4, pro, and VNTI database)
Japanese language option for the entire interface.
Native Linux support.
Highlighting of matches for searches in both the view and the relevant scroll bar.
Opening of previously generated alignments in SnapGene Viewer.
Support for the following GenBank feature types:
assembly_gap
centromere
regulatory
telomere
Support for the following GenBank feature qualifiers:
/altitude
/calculated_mol_wt
/gap_type
/linkage_evidence
/regulatory_class
/type_material
New "Export Selected Protein" command.
New "Analyze Selected Primer(s)" command in the Primers menu, for direction to IDT’s OligoAnalyzer website.
New "Symbols and Abbreviations" window, accessible from the Help menu.
Enhancements:
Improved zooming into selected features and primers when no DNA selection is present.
(Suggested by Sudheendra Rao)
Configured the default behavior to open documents and windows on the primary display, or if other windows have been opened, on the last display that was used.
(Requested by John)
Added the ability to detect common features in inserted sequences.
(Suggested by Tian Chi)
Modified the Add|Import|Detect Features|Primers dialogs to remember the last column used for sorting.
(Suggested by John Hawkins)
Modified the Import Primer from a List dialog to choose by default the last list used.
(Suggested by John Hawkins)
Enabled drag and drop for opening files in the launch dialog, or loading files in an action dialog, or aligning sequences with the alignment list box.
Enabled export of all primer data if no primers are selected.
Enhanced export of primer data to include options for primer length, % GC, and MW.
Improved the default name used by the New File from Selection dialog in many contexts.
Added tooltips to the type and qualifier controls in the feature dialogs.
Improved the detection of regulatory features.
Improved topology detection when using the New DNA File dialog.
Improved sequence trace quality estimation.
Turned off the default prioritization for display of newly created features.
Improved the default phosphorylation of newly created sequences.
Improved the detection of common features by their protein translation in situations where the first or last amino acid may not be present in a relevant match.
Enabled copying of the translation of two or more consecutive segments in a feature, even if the segments are separated by an intron.
Enabled the simultaneous editing of the display priority for multiple features at a time.
Added recognition for Spacebar as a command to page down in all views.
Enhanced the topology indicator to bring up the Circularize or Linearize dialog.
Added a "User Guide" link to the Help menu.
Implemented numerous optimizations and textual enhancements.
Fixes:
Improved the display of aligned sequences that have long names containing carriage returns.
(Reported by Itai Toker)
Ensured that the "Circularize" command will work after amplifying a fragment that began at the numerical origin.
(Reported by Jordan Ang)
Prevented an occasional issue in which multiple copies of a feature were annotated when detecting common features.
(Reported by Leonid)
Enhanced the Gateway simulator to record custom names of Entry clones in the history.
(Reported by Andreas Brodehl)
Ensured that qualifiers are displayed properly when printing Features and Primers views.
(Reported by Gabriele Kleiner)
Improved the MacVector importer to decode all features as features rather than colored ranges, and to decode qualifiers and feature names more reliably.
(Reported by Brandon Paul Weasner)
Improved the alignment algorithm to reduce the likelihood of displaying an unwanted alignment with a large gap.
(Reported by Wulf Dirk and Megha Rajendran)
Removed an outdated note about DTT from the enzyme description for BsmBI.
(Reported by Veadi Tliad)
Fixed issues with printing agarose gels on Windows.
(Reported by Wulf Dirk)
Prevented an occasional issue in which spin boxes would be gray rather than showing the current value.
(Reported by John Murray)
Enabled SnapGene to tolerate and ignore dashes when opening FASTA files.
(Reported by Michael Jepperson)
Substituted estimated quality data for nonsensical embedded quality data that is present in some otherwise valid sequence trace files, and enabled alignment of those sequence traces.
(Reported by Shoma Tsubota)
Fixed an issue where empty lines with tabs or spaces resulted in an erronous message being displayed when importing primers from a list.
(Reported by Hugo de Jonge)
Fixed various alignment issues.
(Reported by Leslie Bembinster and Mily Ron)
Fixed an issue where the bases in sequence view could jump around when using a Windows computers with multiple screens.
(Reported by Warren Wakarchuk and Janel Lape)
Fixed a issue where Copy or Copy Translation did not work after closing another document.
Corrected a minor issue that could arise if a large double stranded selection included 5' or 3' overhangs on both the upstream and downstream ends of the sequence, resulting in the wrong length being reported when requesting confirmation before removing the selected DNA.
Improved the display of sticky ends in Map view.
Enabled Undo/Redo and Copy commands while using the Edit DNA Ends dialog.
Improved the vertical placement of feature tooltips in linear maps when mousing over feature names placed above the strand.
Fixed a few search issues that could arise occasionally.
Improved the import of primers from a list to recognize the 5' phosphorylation state and no longer include this item in the primer description.
Relaxed the format restrictions for accession numbers when importing from GenBank.
Fixed an issue where features with no color were displayed poorly in circular maps when feature labels were togged off.
Prevented "Set DNA Color" from being enabled in read-only contexts such as cloning dialogs.
Improved the behavior of the "Insert Symbol" window on Mac OS X.
Ensured logical updating of feature numbering after checking "Consecutive for all segments" in the Feature Translation Options dialog.
Prevented the unnecessary display of bent connector lines for some enzyme, feature, and primer names placed outside of circular maps.
Ensured that the default author is used for files pasted into the New DNA File dialog even if the copied content is in FASTA, GenBank, or another rich format.
Prevented the occasional placement of feature names too close to each other in circular maps.
Restored the display of a yellow box indicating that one or more features could not be shown in a circular map.
Fixed an issue with the default name when pasting FASTA content into the New DNA File dialog.
Prevented a rare search failure for protein searches in run-on feature translations that wrap around the numerical origin and never hit a stop codon or another feature.
Fixed an issue with the default set of ladders and default ladder.
Fixed an issue where the number of matches for an exact degenerate query (e.g. "N") was not always shown even when the # of matches was not exceedingly large.

New in SnapGene 2.8.3 (Nov 1, 2015)

New Functionality:
Beta version of the Japanese interface. In the Launch dialog, click Help → Language → Japanese.
Enhancements:
When editing references, clicking the "PubMed ID" field now auto selects the contents to make changing the value easier.
The "new version available" dialog was streamlined.
If your support contract has expired, we only inform you about major releases, not bug fix releases.
The Gateway donor vector pDONR222 was added.
Added 80 new features to the common features database.
Fixes:
Fixed an issue that prevented opening some older .dna files.
(Reported by Benoit Moindrot)
Fixed an issue that sometimes prevented performing Gibson Assembly and In-Fusion cloning when the template(s) had sticky overhangs.
(Reported by Gerard Krogt)
Fixed an issue that could prevent Gibson Assembly or In-Fusion cloning when manually specifying the direction of inserts.
(Reported by John Murray).
Improved the display of flipped and unflipped orientations of fragments in the Gibson Assembly or In-Fusion Cloning product tab.
(Reported by John Murray)
Fixed an issue with printing the page header for Features and Primers views when also printing History view.
(Reported by Karl Brune)
Improved the behavior of action dialogs that employ PCR when part of the DNA is selected.
(Reported by John Murray)
Enhanced the alignment algorithm to avoid displaying a suboptimal alignment.
(Reported by Robert Getty)
Fixed a stability issue when pressing or releasing keys.
Fixed a stability issue when exiting the Add/Edit/Duplicate Feature dialogs.
Ensured proper detection of software updates that are available only by renewing your service contract.
Ensured recognition of bottom strand underhangs when using the "To Uppercase/Lowercase" commands.
Ensured proper identification of the OS name for Windows 10 and OS X El Capitan when sending anonymous statistics.
Fixed a glitch where temporary files could contain multiple copies of sequence data and search indexes.
Fixed a rare issue where the Gibson Assembly and In-Fusion dialogs would generate and attempt to display a product when the ends did not actually overlap.
Prevented a potential issue with remembering the last used directory.
Enabled PCR in various circumstances when using a primer that can hybridize to either strand.
Improved protein searches to return matches that lie partially or entirely within a run-on translation.
Enabled the BLAST commands to be invoked while using the Description Panel.
Ensured that the selection in the Sequence view minimap always matches the sequence selection after interacting with an aligned sequence.
Fixed an issue where an aligned sequence and associated feature translations might not be displayed properly after modifying the reference sequence.
Improved the vertical appearance of the "Preview/Next Aligned Region" buttons when viewing an expanded aligned sequence.
Improved feature display when scrolling between regions of expanded alignments.
Fixed an issue where certain features did not display properly in circular maps.
Enabled robust copying and pasting into Apple Mail.
Ensured that PubMed ID's would not be truncated when pasting into the Edit References dialog if leading spaces had been copied to the clipboard.

New in SnapGene 2.8.2 (Aug 17, 2015)

New in SnapGene 2.8.1 (Jul 17, 2015)

New in SnapGene 2.8.0 (Jul 2, 2015)

New Functionality:
Added an interactive minimap overview to Sequence view.
Enabled Map view to display either external plus internal feature labels, or only internal feature labels, or no feature labels.
Added a "Splice to Remove Introns" command.
Enabled cloning and PCR dialogs to remain open after generating the product, so that related procedures can be simulated quickly and easily.
(Requested by Alejandro Sarrion)
Modified the Insert Fragment(s) dialogs to enable digestion of a linear vector.
(Requested by David Bikard and Seth Goldman)
Enabled individual features to be prioritized for display in maps.
(Requested by Guiliang Tang, Ignacio Ferrés, Goran, and Thomas Branson)
Added a "Delete Trimmed Bases" command for cleaning up the display of alignments.
(Inspired by Michael Lynge Nielsen)
Modified the display of aligned sequences in Map view to show insertions as inverted triangles.
(Requested by Michael Lynge Nielsen)
Enabled maps and history to be exported as grayscale images.
(Requested by Jennifer Tomczak and Novozymes)
Added a "Hide Aligned Sequence" context menu command for Map and Sequence views.
Added Lowest, Lower, Higher, and Highest stringency trimming options for aligned sequence traces.
(Requested by Wulf Dirk)
Added an "Open Recent" cascading menu to the top toolbar and the Dock menu on OS X.
Added an "Import from GenBank" command to the Dock menu on OS X.
Added a "Copy Map Label" context menu action.
Added a three finger tap gesture to look up enzyme information without modifying the selection.
Enabled bzip2 (bz2) compressed content to be opened directly.
Enhancements:
Improved history colors when flipping the sequence, adjusting the numerical origin, renumbering the bases, or changing the methylation.
(Suggested by Devin Strickland)
Moved the aligned sequence tooltips in Map view to above the aligned sequences.
(Suggested by Karl Brune)
Improved the display of alignment gaps in Map view.
Sped up starting the application and showing manipulation dialogs.
Dramatically sped up the decoding of large archive files.
Sped up topology detection.
Sped up the opening of gzip (gz) compressed content.
Improved the opening of large FASTA archives and gz files.
Added file icons for the "Please choose", "Recent Files", and Windows menus.
Listed keyboard shortcuts in the Find menu.
Enhanced primer names and stems to turn red when mousing over an alternative binding site.
Modified Map view to show the sequence as two strands when custom DNA colors are visible.
Added "GenScript" to the Sequence Author list.
Added O'RangeRuler™ ladders from Thermo Scientific.
Added UBPBio ladders.
Updated the restriction enzymes and common features databases.
Various textual, color, and alignment enhancements.
Fixes:
Fixed a rare issue where the application could hang if an aligned sequence had no trace data and began with a non-matching N.
(Reported by Arthur Fridman)
Improved the import of very large archives.
(Reported by Tamunonengiye-Ofori Lawson)
Enabled copy/paste of a primer-primer selection as a Find query.
(Reported by Michael Lynge Nielsen)
Improved the behavior of the "Replace Original with Aligned" command.
(Reported by Sarah Prewitt)
Fixed various issues with displaying restriction sites when viewing a primer binding site in a circular sequence near the numerical origin in the Add/Edit/Duplicate Primer dialogs.
(Reported by Devin Strickland)
Fixed a stability issue if the current license expires while the software is in use.
Accelerated the display of feature pliancy and selection in Lines mode of Enzymes view.
Improved the import of text files with non-UTF file encodings (e.g., MacRoman).
Configured an Undo of a sequence edit to clear prior "Find" results.
Modified the behavior of the Back/Forward buttons in the Restriction Enzymes dialog to be simpler and more logical.
Prevented auto-complete from inappropriately listing headings and actions in the Sequence Author control in the Description Panel.
Fixed a stability issue when opening a .dna file not created with SnapGene.
Fixed a stability issue when moving, copying, and deleting files.
Prevented prior history colors from remaining visible after Undo of a sequence edit.
Ensured that an unsaved set of chosen enzymes will always be restored when opening a document.
Fixed a rare stability issue with showing the Genetic Codes dialog.
Fixed a stability issue with computing translations for features with introns.
Removed duplicate entries in the "Choose from" menu in the "Choose Enzymes" dialog.
Fixed a rare issue where a download progress dialog could be shown while the New Version Available window is visible.
Fixed a stability issue when using a context menu to remove an aligned sequence.
(Reported by Karl Brune)
Made the Make/Edit/Duplicate Primer dialogs more compressible so that they fit completely on small screens.
(Reported by Kasey Day)
Fixed a rare stability issue.
Improved “primer” feature import from VNTI .ma4 archives to show the imported items as primers.
Ensured focus transfer to the next window down when the top window is closed.

New in SnapGene 2.7.3 (May 29, 2015)

New in SnapGene 2.7.2 (Apr 23, 2015)

Enhancements:
You can now use Cmd+D on Mac to activate "Don't Save" when attempting to close a file with unsaved changes.
Added MW Markers from Axygen
Added MW Markers from Biozym
Improved detection of lacZ-alpha.
Improved default placement of windows.
Bug Fixes:
Fixed a crash that could occur while using the Simulate Agarose Gel dialog and switching between showing simplified and full primer duplex structures.
Fixed a regression where the option of regenerating the enzymes used to digest the vector was not offered when designing primers for InFusion® cloning.
Fixed a bug where unsaved annotations were not reflected in history or transferred to the product when using a fragment directly when simulating Gibson Assembly or InFusion cloning.
Fixed a bug with showing some primer binding sites.
Fixed a bug where designed primers sometimes did not use the desired and required Tm.
Fixed a bug that prevented simulating Gibson Assembly using fragments(s) with 3' A or G overhangs.
Fixed a bug that resulted in an incorrectly genereated Entry Clone when linearizing the attB insert within the BP and BP + LR cloning dilaogs.
Fixed a bug that sometimes prevented simulating BP cloning when digesting the BP insert with an enzyme that cuts multiple times.
Removed a partially shown color button in the side toolbar of the Primer and Edit DNA Ends dialogs.
Fixed a bug that prevented attempting to destroy a restriction site at the numerical origin by selecting it and pressing the Delete key.
Updated KflI to indicate it is not Dcm methylation sensitive.
Fixed a crash that could occur after returning to interact with History view after resurrecting an ancestral sequence.
Fixed the crasher reporter Mac OS X Yosemite.
Fixed a potential crash in Features and Primers views when modifying annotations.
Hide the color mode and visibility controls in the Map & Sequence Options dialog when using an embedded sequence, e.g. while using a cloning dialog.
Fixed a bug where using a mouse wheel to scroll up or down after showing the zoom controls but not zooming could result exiting out of zoomed mode.
Fixed a bug where it was not possible to click on feature names outside a circular map or above a linear map if shown enzymes and primers were both turned off.
Fixed a bug where if using Gibson assembly to assemble a linear product, if the first amplified fragment wrapped around the numerical origin the product was incorrectly shifted and circular.
Fixed a bug where if using Gibson Assembly to assemble a linear product, sticky overhangs and endpoint modifications in the first and last fragment were not properly migrate to the product.
Fixed a bug that prevented using Gibson Assembly to assemble a linear product if either end of the product was covalently closed.

New in SnapGene 2.7.1 (Mar 7, 2015)

New in SnapGene 2.7.0 (Mar 6, 2015)

New Functionality:
Substantially improved look and feel on retina displays.
DNA colors
Primers colors
Edit multiple primers
Added Copied Primers (Cmd+Opt+R)
(Requested by Karl Brune)
Simulate assembling fragments via Gibson Assembly
(Requested by Vincent Gaggioli)
Added warnings for out of frame translated features when overlapping, assembling, or ligating one or more fragments.
You can now paste GenBank, EMBL, or FASTA encoded content into the New DNA File and Insert|Replace Bases dialogs. Annotations will be preserved as if you had opened a gb/embl/fa file directly. Similarly you can now align with a copied FASTA, GenBank or EMBL sequence. The default name for a pasted New DNA File or aligned copied sequence has also been improved.
(Requested by Allan Drummond, Karl Brune, Cornelius Miething, and Christel Aebischer)
Open DNADynamo files
(Requested by Maria Deak)
Open gzip compressed content (e.g. .fa.gz)
When simulating an agarose gel, you can now copy the gel image or fragment list.
(Requested by Wulf Dirk)
Expanded the range of agarose concentrations supported when simulating gels.
(Requested by Robert Getty)
Added numerous MW Ladders.
(NZYTech ladders requested by Daniel Osório)
(PHENIX Research ladders requested by Robert Getty)
You can now make feature(s) from selected aligned sequence(s)" via a new "Make Feature[s] from Selected Sequence[s]" command in the "Aligned Sequences" menu.
(Suggested by Andy Crouse)
Added "Enter|Exit Full Screen" commands to the Window menu on OS X.
Added a "Show Chromatogram Data" context menu command for aligned sequence traces.
Added "Copy Feature Name" and "Copy Primer Name" context menu actions.
(Requested by Wulf Dirk)
Added a window list to the Dock menu on OS X.
(Requested by Di )
Added commands to the jump list shown when right clicking the application in the taskbar on Windows 7 and later.
Enhancements:
Improved detection of lacZα
(Requested by Joëlle Fourment)
When mousing over an enzyme that cuts more than once, the stem connected other restriction sites now also turn red.
(Suggested by Angika Basant)
Reduced the size of text and features in History view maps to facilitiate showing more annotations in the shrunken maps.
(Inspired by Damien Douchi)
Added an option on Windows to automatically minimize the Launch window when all windows have been closed.
(Suggested by Ron Godiska)
Added the "NEB Stable" transformation strain.
(Requested by András Tálas)
You can now select gaps within features by Opt/Alt+clicking them.
Prevent TOPO TA cloning with primers that are phosphorylated.
Updated the TA "TOPO" and Gateway Donor vectors.
The ruler shown for translated features in Sequence view now shows a break if there is a discontinuity in the translation numbering.
Removed the "Enzymes" tab from the TA and GC cloning dialogs since restriction enzymes are never used.
Added a "PCR and Mutagenesis Tutorial Video" command to the "Actions" menu.
Improved the visibility of warnings shown within the status box at the lower right of manipulation dialogs.
Improved display of ladder fragment lengths in simulated agarose gels.
Added Cmd+Shift+[, Cmd+Shift+], and Cmd+Shift+# to switch lanes in the Agarose gel dialog. You can now use the swipe gesture as well.
When changing the % agarose concentration the fragments now animate to their new position.
Improved look and feel on OS X Yosemite. Unfortunately we can no longer support OS X Leopard and Snow Leopard.
SnapGene is now a 64 bit application on Mac OS X.
Extensive icon, textual, color, and rendering enhancements.
Added support for queueing when using a shared license.
Bug Fixes:
Fixed a bug where when importing primers from a list, if the primers list began with a "Name Sequence" line an error message would be shown before proceeding with showing the Add Primers dialog.
(Reported by Pascal Drevet)
Fixed a bug that prevented shifting clicking letter codes from two different translated in-frame features.
(Reported by Rocky Cranenburgh)
Fixed a bug that prevented importing primers containing U's or I's from a list.
(Reported by Stephanie Ruiz)
Fixed bugs with opening and pasting DNA sequences containing colons and other punctuation.
(Reported by Ron Godiska)
Fixed bugs with displaying origin-spanning and other complex multiple sequence alignments.
(Reported by Pavel Chubukov, Chris Katanski, and Jenna Christensen)
Fixed a crash when opening files with a one or more blank lines at the top.
(Reported by Monfort Pineda Asun)
Fixed a bug where the Save As dialog sometimes did not default to the correct filename on OS X 10.9 and 10.10.
(Reported by Nick Bogard)
Improved importing primers from a Vector NTI database and GenBank files exported from Vector NTI.
(Reported by Cor Breukel)
Fixed a bug where printing an agarose gel the length of amplified fragments was not listed.
(Reported by Alice Fok)
Fixed a bug with simulating Gibson Assembly with one or more fragments with 5' overhangs.
(Reported by Shouqiang Cheng)
Fixed a bug with simulating InFusion Cloning with one or more fragments with 3' overhangs.
Fixed a bug where when toggling the "5' Phosphorylated" checkbox in the Make/Edit/Duplicate Primer dialogs, the melting temperature was not recomputed.
SnapGene now refuses to open bz2 compressed content.
Fixed a bug that could result in a hang when trying to find data within an empty file.
Fixed a bug with showing history colors after deleting an arbitrary range of bases.
Fixed a bug where various Edit menu actions (e.g. "Copy Top Strand") sometimes were not be enabled when a selection was present.
Fixed a crash that can occur if you rename, move, or delete a file while it was open and you were using a modal dialog (e.g. Edit Primers).
Fixed a bug that prevented pliancy from being shown for inserts in the TA and restriction cloning overviews.
Fixed a bug where a non-specified gateway vector was shown in black instead of gray in the cloning overview.
Fixed a bug where after changing the transformation strain the "Hide/Erase" button in History view did not become enabled.
Fixed a bug where tooltips shown in the New/Insert/Replace Dialog and a few other places would continue to be shown if the window containing the associated label was hidden or closed while the tooltip was visible.
(Reported by Melissa Stokes)
Improved file association registration on Mac OS X.
Fixed a bug where when displaying a reverse aligned sequence as a double stranded sequence the DNA shown could be incorrect.
Fixed a bug that could result in a crash if you closed a document while using the Edit and Duplicate Primer dialogs.
Fixed a crash that could occur when closing an open document with unsaved changes that is currently in use in a manipulation dialog.
Turned off changing a combo box selection using the mouse wheel.
Fixed a bug that prevented restriction sites close to the numerical origin from being shown in History view.
Fixed a bug with showing partial filling in when using the "Choose dNTPs" dialog.
You can now use Cmd+Shift+[5-9] to switch to such tabs in cloning dialogs that have many tabs.
Fixed a bug that prevented drag selecting from a site in main view in Enzymes view to a site in the mini map or vice versa.
Fixed a bug where agarose gel fragment endpoints were not printed correctly when the template was set to count from something other than 1.
Fixed a crash that could occur when pressing the left arrow key when a button has focus.
Fixed a crash that result from use core search algorithms.
Fixed a bug in Map and History views where using the "Edit Map Label" and other context menu commands sometimes resulted in the map being copied tot he clipboard as well.

New in SnapGene 2.6.2 (Dec 19, 2014)

New in SnapGene 2.6.1 (Dec 11, 2014)

New in SnapGene 2.6.0 (Dec 3, 2014)

New Functionality:
TA, GC and UA cloning.
Support for U's in DNA sequences.
You can now edit the color, type, directionality, and translated state for multiple features at a time.
(Requested by Tian Chi and Wulf Dirk)
Non aligned ends are now shown when viewing alignments in Map view.
(Requested by Devin Strickland, Bryan Strouse, and Janel Lape)
All mutations are now visible when viewing alignments in Map view.
(Suggested by Wulf Dirk)
You can now linearize a circular sequence at the location of a placed cursor.
(Requested by Diane Chauliac)
You can now directly circularize a selected restriction fragment. When attempting to circularize a PCR product with single 3' base overhangs, SnapGene now offers to remove those overhangs in order to make circularization possible. Finally, history colors are now generated when circularizing.
(Requested by Dan Kraut)
You can now export Map and History views at various resolutions. Improved support exporting transparent images. When exporting as TIFF, SnapGene now uses LZW compression and transparent TIFF's are now also supported.
You can now export Map view, History view, and agarose gels to the EMF vector format on Windows.
When copying a map or history to the clipboard a vector form of the data is now stored on the clipboard so elements can be moved or edited when pasting into programs like Microsoft Office or Adobe Illustrator.
Open EMBL formatted sequences and export sequences using the EMBL format.
(Requested by Iñigo Lasa, Colin Adrain, and Kobi Benenson)
You can now export sequences to the DDBJ format.
Added "λ DNA – HindIII/φX174 DNA – HaeIII Digest" ladder
(Requested by Brian Ayre)
Enhancements:
SnapGene can now automatically annotate common features when opening FASTA sequences and archives.
(Suggested by Willem-Jan Waterreus)
The "Anneal Oligos" dialog now auto populates if two primers are selected in an open sequence when the window is shown.
You can now include features added by NCBI when importing from GenBank.
Added the full template name to the tooltip shown when mousing over the list in the Simulate Agarose Gel dialog if the name is truncated within the list.
When exporting History view to PDF, we now use Portrait instead of Landscape orientation since it usually fits better that way.
Improved the default size of the "Manage Enzyme Sets" dialog.
After linearizing at any position other than the origin, Map view now defaults to showing a broken circle.
Various font, color, and textual enhancements.
Bug Fixes:
Fixed a bug that could prevent printing with network printers on Windows.
(Reported by Cassandra Diegel)
Improved exporting to GenBank to better conform to the standard and resolve various warnings when converting to EMBL when uploading files to EMBL-EBI.
(Reported by Kobi Benenson)
Fixed a bug where trace data for short aligned sequences could be shown at too low a resolution.
(Reported by Miguel Cardoso de Brito)
Fixed a bug that could result in primers not being transferred to an amplified product when using PCR based dialogs.
(Reported by Mathias Friedrich)
Fixed a bug that prevented opening some MacVector files.
(Reported by Hilary)
Fixed a crash that could occur while simulating various manipulations.
(Reported by Angika Basant)
Fixed bugs with visualizing insertions at the numerical origin and replacing the original with the aligned sequence under such circumstances.
(Reported by Jason Niehaus)
Fixed a bug where if no attB inserts are to be amplified by PCR, when clicking "Choose attB Primers" SnapGene should pop up a message instead of doing nothing.
Fixed a bug with deselecting primers in Primers view by Cmd/Ctrl clicking.
Fixed a bug where primers were lost when using the "Replace Original with Aligned -> Make New File" command.
Fixed a bug with replacing and existing license file on Windows.
Fixed an erroneous error message that would show up (invalid license file) if installing the license file fails.
Improved exporting to SVG. (The bounds of the exported content are not set so scrolling, if necessary, is much improved).
Fixed a bug that resulted in "Copy Map" to sometimes be disabled while viewing Map view.
Fixed a bug where the default filename when using Save As was sometimes incorrectly set to "Untitled" on Mac OS X 10.9 and later.
Fixed a bug that prevented opening GenBank files when filtering files in the Open File dialog to "Sequence Files".
Fixed a bug where when simulating a manipulation using an open document with unsaved case changes, those changes were not reflected in a resurrected ancestor.
Fixed a bug where unsaved case changes were not properly reflected when exporting to FASTA or plain text.
Fixed a bug when annealing oligos I's were not converted to N's as expected.
Fixed a hang when deleting bases from a single strand from an end that is currently covalently closed while using the Edit DNA Ends dialog.
Fixed a bug where when enlarging the Edit DNA Ends dialog, additional space not used entirely for viewing the upstream and downstream ends.
Fixed a bug where if a mixture of colored and non-colored features were selected when triggering "Features -> Feature Color" no option should be checked by default.
Fixed a cosmetic glitches with rendering ovals and header buttons.
Fixed a bug where an error message was shown twice when trying to open a GenBank file that does not contain a nucleotide sequence.
Fixed a crash that could occur when importing a GenBank archive that contains on or more empty sequences (aka sequences without nucleotide data).
Fixed a crash that could occur while viewing raw sequence trace data.
Fixed a bug where if enzymes were off and you opened and then canceled out of the Choose Enzymes dialog SnapGene would offer to turn on showing enzymes.
Various stability fixes.
Fixed various memory leaks.

New in SnapGene 2.5.0 (Sep 10, 2014)

New Functionality:
Gateway Cloning
You can now insert or ligate up to eight restriction fragments.
(Requested by Stefanie Ranf and Daniel Leadbeater)
You can now overlap up to eight fragments when performing Overlap Extension PCR.
(Suggested by Ben Draper)
InFusion Cloning now supports up to 8 fragments.
(Requested by Michael Lynge Nielsen)
Print or export an inverted agarose gel.
(Requested by Mei Li and Eric Lambie)
Import a Range of Records from GenBank.
(Requested by Petar Todorov)
Import a region of a sequence from GenBank.
(Requested by Luke)
Import one or more primers copied to the clipboard.
(Requested by Karl Brune)
Improved importing from Vector NTI Databases and ma4 archives to include sequence history, creation and modification dates, the sequence author, user comments, as well as maintain the creation / modification date and time in the resulting .dna files that are produced.
(Requested by Novozymes)
Added Thermo Scientific's "GeneRuler™ High Range DNA Ladder"
(Requested by Nathan Sweeney)
Added KAPA Biosystems' Express and Universal ladders.
(Requested by Pengguna Saja)
Added Fisher Scientific Ladders.
(Requested by Gavin Johnson)
Added SERVA DNA Ladders.
(Requested by Philipp)
Added Thermo Scientific's MassRuler ladders.
(Requested by Riadh Lobbardi)
Enhancements:
Reorganized the Choose Restriction Enzymes dialog to make it easier to find/use the controls for automatically select enzymes based on a criteria.
The number of binding sites are now shown in primer tooltips.
(Requested by Karl Brune)
Increased the maximum number of recent documents listed to 25.
(Requested by Karl Brune)
Enhanced the GenBank importer to decode base numbering if specified in a REGION indicator within the ACCESSION section.
SnapGene can now open malformed GenBank files produced by Vector NTI Express.
(Requested by Kathy Koprivnikar)
Added a yellow warning to the Add/Edit/Duplicate Primer dialogs when a primer has multiple binding sites.
(Suggested by Devin Strickland)
Enhanced the look and feel of directionality buttons when a window loses focus.
Now decoding /Design_Description qualifiers in VNTI files as /note qualifiers.
Improved the mouse cursor while over or dragging a splitter.
Improved Actions menu layout.
Various optimizations, textual and tooltip enhancements.
Bug Fixes:
Fixed a bug where selected non-cutters were not listed when printing Agarose Gels.
(Reported by Kasey Day)
Fixed a bug where feature names could overlap each other in circular maps.
(Reported by Dan Strongin)
Fixed various bugs with creating features from an enzyme selection whose right end is the numerical origin.
(Reported by Pieter J. de Jong)
Fixed a bug where full-sequence "source" type features were changed to "misc_feature" when exported using the Vector NTI GenBank format.
(Reported by Wulf Dirk)
Fixed a bug with copying while using the Edit and Duplicate Primer dialogs.
(Reported by Byung Ouk Park)
Fixed a bug that could result in bogus primers being shown for the current sequence in History View and a crash that could occur while interacting with these bogus elements.
(Reported by Alok Shenoy)
Fixed a potential hang that could occur while importing VectorNTI databases.
Fixed a bug where after editing the list of MW markers, the pull down menu did not resize.
When closing a window, the next visible window is now automatically active.
Fixed a bug where when saved enzymes sets were modified, these changes were not shown in an already open PCR, Overlap Extension PCR, Mutagenesis, InFusion Cloning, or Gibson Assembly dialog.
Fixed a weird glitch where buttons in the launch dialog in addition to others would appear to disappear when the window lost focus.
Fixed a bug that prevented the Cmd+[ and Cmd+[ shortcuts from activating the Back/Forward buttons in the Restriction Enzymes dialog.
Fixed a bug where copying from the primer sequence controls copied invisible formatting to the clipboard.
SnapGene now refuses to open GenBank Protein sequences, informing the user that they are not yet supported at this time.
Fixed a regression with drawing rounded ovals used for example for mouse position indicators.
If a custom map label is used in Map View, we now use that custom map label for the root node in History View as well.
Fixed a crash that could occur when performing range limited a highly degenerate MICA search.
Fixed a bug that prevented alignment directionality symbols from showing up properly when printed to PDF on 10.9.
Fixed various glitches with printing the aligned sequences summary when printing Sequence View.
SnapGene now opens sequences full screen more smoothly on Mac OS X.
Fixed a bug that could result in aligned sequences reporting incorrect dates.
Fixed various bugs with pressing and releasing Opt/Alt and updating menu actions.
Fixed a regression that prevented "Go To" from working while viewing a sequence trace.
Fixed various bugs with printing zoomed alignments.
Fixed a bug that prevented "Replace Original with Aligned Sequences" from proceeding when using two more compatible aligned sequences if some but not all align around the numerical origin.
Fixed a bug that could cause a list selection to change when activating a window on Mac OS X.
Fixed a bug where when selecting an externally placed feature name in map view, the wrong DNA range was selected.
Fixed various bugs with viewing origin-spanning alignments as double stranded sequences.
Fixed a potential crash that could occur while trying to print on Mac OS X.
Fixed a crash that could occur while using Sequence View.
Fixed a crash that could occur while simulating agarose gels.

New in SnapGene 2.4.3 (Jul 3, 2014)

New in SnapGene 2.4.2 (Jun 13, 2014)

New in SnapGene 2.4.1 (Jun 10, 2014)

New in SnapGene 2.4 (May 29, 2014)

New Functionality:
A 5’ overhang can be blunted by either filling in or chewing back. (Requested by Berislav Lisnic and Andreas Toft Sorensen)
A DNA sequence can be exported to a GenBank-style file that is optimized for import into Vector NTI®. (Requested by Wulf Dirk Leuschner, Scott Dooley and Alper)
Clone Manager individual primer files (.pd4) can be opened directly, and primer collection files (.px5) can be used for import into SnapGene. (Requested by Oliver Sinfield and Jo Marie Bacusmo)
You can now manually trim an aligned sequence by selecting the range to be trimmed off, then clicking "Aligned Sequences -> Trim Selected Range". (Inspired by Alex Zelenskyy)
You can now linearly ligate up to four fragments. (Requested by Emmanouil)
You can now search for the amino acid "X" by using quotes. (Requested by Keoni Gandall)
The MW of amino acid selections are now show in the selection bar. (Requested by Deepak Patil)
For a feature in the first row of a map, if there is not enough room to show the name within or along side the feature, the name is now displayed outside the map.
History View now displays how a sticky end was blunted.
History View now lists the names of primers used during PCR.
When features or primers are viewed in a DNA file, imported from a list, or when detecting common features, a new button at the top left provides options for quickly checking and unchecking the listed items.
If you hold Alt/Opt, you can now "Copy Transparent Map" or "Copy Transparent History". This works for the Edit menu, the top toolbar button menu, and right click context menus in Map and History views.
Enhancements:
Improved detection of Gateway recombination sequences.
Improved opening of GenBank files exported by Vector NTI including sequence name, author, creation and modification dates, and feature names.
Improved opening of GenBank files exported by Serial Cloner including feature visibility, names, colors, directionality, and descriptions.
Improved support for QHD displays on Windows.
When exporting the default directory is now the last directory content was exported to. In addition the last format used is now the default format. (Suggested by Wulf Dirk)
The yellow messages that indicate a number of enzymes, features, or primers are not displayed on map view due to limited space now show a tooltip when moused over that indicates which enzymes, features, or primers could not be shown.
Added support for the "Candidate Division SR1 and Gracilibacteria" genetic code.
Sped up alignments of fairly large sequences (e.g. 40 Kbp) against very large reference sequences (e.g. chromosomes).
Added links to Translations and Alignments tutorial videos.
Various color and textual enhancements.
Bug Fixes:
Fixed glitches with opening GenBank files that contain tab characters. (Reported by Wulf Dirk)
Improved decoding feature names from GenBank files. (Suggested buy Wulf Dirk)
Fixed a bug where features might not be transferred to the product when simulating PCR using overlapping primers that mutagenize the sequence. (Reported by Dan Kraut)
Fixed a bug where PCR based dialogs would sometimes complain that a primer pair was not suitable for PCR when despite overlapping binding sites PCR was possible because the template was circular. (Reported by Dan Kraut)
Removed nonfunctioning File and Edit menus from Make/Edit/Duplicate Primer dialogs on Windows. (Reported by Scott Dooley)
Fixed a bug where if a non-native file was chosen as the template or vector in any of the manipulation dialogs, features would not be transferred to the product while simulating cloning, PCR, etc. (Reported by Rocky Cranenburgh)
Fixed a bug where long sequence and ancestral sequence names could be cut off when shown in History View. (Reported by Alok Shenoy)
Fixed detecting custom 7 and 8 bp custom common features. (Reported by Donelson)
Fixed issues with annotations are not shown, would you like to display them type messages on Windows. (Reported by Wulf Dirk)
Fixed a bug where horizontal scrolling switched tabs in the Preferences, Map & Sequence Options, Primer and Chromatogram Data dialogs.
Disabled the "Select All" button while using the "Add Features/Primers" and "Detect Common Features" dialogs since selections are not allowed.
Fixed a bug that made it impossible to use a non-native file as the vector in the InFusion Cloning and Gibson Assembly dialogs.
Fixed a bug that could result in a crash when editing feature translation options for 1 and 2 bp features.
No longer listing translation qualifiers (codon_start, transl_table, translation) in Features View for features that are not marked for translating in Sequence View.
Fixed various bugs with opening some rich text encoded files.
"Apply this genetic code to existing features" did not properly update feature translations, mark the sequence as modified, or support Undo/Redo.
Fixed a glitch where an empty COMMENT or DEFINITION was sometimes exported to GenBank formats.
The "Reset Warnings" button in the Preferences dialog is now disabled if no warnings have been turned off.
Fixed a bug that resulted in features now being shown for the current sequence in History View after transforming into another strain, changing the methylation, or other changes that don't result in actually changing the underlying DNA.
Disabled "Edit -> Select Range" while using the Detect Common Features and Import Features/Primers dialogs.
Fixed various glitches with shift-clicking fragments while using the Simulate Agarose Gel dialog.
Fixed the MW for amino acids "X" and "B"
Fixed a bug where history colors might now shown when using mutagentic primers to simulate PCR.

New in SnapGene 2.3.5 (May 8, 2014)

New in SnapGene 2.3.4 (Apr 24, 2014)

New in SnapGene 2.3.3 (Apr 16, 2014)

New in SnapGene 2.3.2 (Mar 21, 2014)

New in SnapGene 2.3.1 (Mar 21, 2014)

New in SnapGene 2.3 (Mar 13, 2014)

New Functionality:
Aligned sequences can now be trimmed manually.
Features, primers, ORFs are now shown when viewing aligned sequences as double stranded sequences.
Letter codes that overlap discrepancies are now shown in red while viewing aligned sequences as double stranded sequences.
You can now replace bases in the reference sequence using one or more aligned sequences. (Requested by Jared Bailey and Veronique Zennou)
You can now use boolean logic (or, not) when searching for DNA sequences. Added a "Search Tips" dialog that explains how degenerate bases and boolean logic can be used when searching for DNA and protein sequences, as well as how to perform various searches for enzymes, etc.
You can now export an enzyme set as a list. (Suggested by Lynne Harris)
You can now export Noncutters. (Suggested by Devin Strickland)
You can now copy the reverse complement of a primer sequence. (Suggested by Allan Drummond)
Added a variety of alternate commands that are available by holding Alt (Windows) or Opt (Mac). These include: Close All Without Saving  (Suggested by Seth Goldman) Detect Common Features in the Selection  (Suggested by Wulf Dirk) Minimize All Zoom All
Added DNA MW Markers for Bioneer, Canvax Biotech, and Geneaid.
You can now shift/control click aligned sequence arrows at the lower left of Sequence View to select multiple aligned sequences.
You can now deselect restriction sites and primer binding sites by Cmd/Ctrl + clicking.
Enhancements:
You can now click and hold to move aligned sequences up and down, or adjust the enzyme supplier order. (Suggested by Seth Goldman)
You can now set the "Detect Common Features" and "Import Features/Primers from Another File" dialogs to not show details by default. (Suggested by Wulf Dirk Leuschner)
Increased the maximum primer length from 150 to 200 bp. (Requested by Seth Goldman)
Reduced the minimum common feature length from 8 to 6 (Requested by Malon Kit)
Added directionality indicators to features in Sequence View while using infinite scrolling if a features directional endpoint is not visible and space permits.
Speed up loading documents with aligned sequences and showing alignments in general.
Improved and speed up the alignment algorithm
Improved the detect common features algorithm
Improved circular plasmid detection
Improved searching for enzymes
Improved how single-base gaps are shown when viewing aligned traces.
Various optimizations that result in faster loading, zooming, and refreshing linear maps.
Added a "Remove" button at the lower left of the "Browse Common Features" dialog while viewing custom features.
Added "Canvax Biotech" and "Cellecta" to the "Sequence Author" menu in the description panel.
Improved the default set of DNA MW Markers
Added a new "ORFs Only" icon
Improved default focus when using the Simulate Agarose Gel dialog.
Improved right click context menu's for feature/primer name, search, and other text controls.
Added "SnapGene Bucks..." link to SnapGene (Mac) and Help (Windows) menus.
You can now click on ladder and transformation strain names (or methylation information) to check/uncheck them in the Edit Strains/Ladders dialogs.
Scale factors now animate back to 1.0x if clicked while viewing a sequence trace.
Clicking "Preferences" in "Summary of Calculation Methods" now transfers focus to the checked radio button for changing duplex complexity.
Streamlined context menu for "Summary of Calculation Methods" and "License Agreement" dialogs.
Converted the format used for exporting and importing enzyme sets to plain text.
Added links to Gibson Assembly and In-Fusion Cloning tutorial videos to their cascading menus.
Various color, textual and stability enhancements.
Bug Fixes:
Fixed a bug that could prevent many menu actions from being enabled while using the Simulate Agarose Gel dialog. (Reported by David Scalzo)
Fixed a crash that could occur when attempting to import primers from a list or open a sequence archive. (Reported by Oliver Sinfield)
Fixed a glitch that prevented opening some Jellyfish files. (Reported by Joao Goncalves)
Fixed a bug that allowed primer controls to scroll vertically using the mouse wheel or clicking and dragging up and down. Also improved their vertical height. (Reported by Allan Drummond)
Corrected the recognition sequence for FaiI. (Reported by Pieter de Jong)
Fixed a bug with copying an ORF translation if it begins at the end of the sequence but the first letter code is actually one or more bases in from the end. (Reported by Mark Fisher)
Disabled "New File from Selection" for aligned sequence selections.
Fixed a minor bug with showing proper history colors.
Fixed a minor glitch with displaying the base under the mouse in the single line view of the reference sequence in Sequence View while viewing an alignment.
Fixed a minor bug with sorting enzymes by distance from the selection.
Fixed a bug with identifying the selection or placed cursor while viewing an alignment.
Fixed a glitch that could result in some trace data not being displayed while viewing an alignment.
Fixed a minor glitch with refreshing the features menu while using a manipulation dialog.
Fixed a bug that could result in primer phosphate groups not being shown while viewing alignments
Fixed a minor bug that could result in a feature not correctly being reset from using an alternative Start codon when bases were inserted or deleted within the original start codon.
Fixed a bug with exporting aligned sequences other than sequence traces where N's could show up as -'s in the exported DNA file.
Fixed various bugs when viewing an aligned sequence as a double stranded sequence when multiple sequences are aligned.
Fixed a bug with showing the numerical origin when viewing primers that wrap around the numerical origin while using the Add/Edit/Duplicate Primer dialogs.
Fixed a regression that prevented the "Your copy Expires soon" and "Getting Started" dialogs from showing any text.
Fixed a potential crash when computing quality measures when dealing with bad trace data.
Fixed a bug with showing some multiple sequence alignments.
Fixed a bug where when converting part or all of a primer name to upper or lowercase while using the Add/Edit/Duplicate Primer dialogs, the shown binding site was not updated.
Fixed a bug with displaying the cursor when placed at the right edge of an aligned sequence.
Fixed glitches that occurred if you tried to move the cursor or move or extend the selection in an aligned sequence such that it extends or is outside the aligned range.
Fixed a glitch where when moving the cursor to the very right of the aligned range while viewing an aligned sequence as a double stranded sequence, the view would scroll to the very beginning.
Fixed a bug where while using Sequence View with infinite scrolling and zooming in it was possible to scroll too far to the right.
Fixed a bug where newly created files (E.g. New File or manipulation products), if you modified them after they were opened, then undid the change, the window lost it's "modified" state and didn't ask if you wish to save before closing as it should, even though all undoable changes had been undone.
Fixed a bug that resulted in a selection being shown for an aligned sequence when shown as double stranded when the selection is just upstream of the trimmed range.
Fixed a bug that prevented showing the green/orange arrows indicating the reading frame for generic translations of aligned sequences.
Fixed a bug where when scrolling far to the right and viewing translations for an aligned sequence some letter codes were painted on top of each other.
Under "Sequence Author", changed "5 Prime" to "5 PRIME".
While viewing an alignment in Sequence View, if you click below the horizontal splitter outside of any aligned sequence, you can once again use the arrow keys to scroll the view, or other key presses to effect the reference sequence.
Fixed bugs with painting generic translations when zooming.
If a subscription license is expiring soon, before showing the expiring soon message, SnapGene first attempts to update the license in case the subscription has been renewed already.
Fixed various bugs with displaying trace data when viewing alignments.
Fixed a bug where if an operation is selected automatically in History View it was not shown as selected, only history colors were shown.
Fixed a bug that prevented propagating methylation changes to aligned sequences.
Fixed the following bugs with reverse aligned sequences: -showing %GC for selections -copying translations
Fixed bugs with dragging selections over gaps while viewing multiple sequence alignments in Sequence View.
Fixed a bug where the numerical origin could be shown incorrectly for aligned sequences
Fixed bugs with displaying selections that wrap-around the numerical origin in Sequence View.
Fixed a bug with highlighted the matched DNA when searching if the last matched base was the first base in the sequence.
Fixed a bug where if multiple DNA modifications are performed while using the Edit DNA Ends dialog, the resulting file would get bigger than it should due to embedding the intermediate ancestors.
Fixed a regression with the mouse position indicator when interacting with the currently sequence map in history view.
Fixed a bug where if a linear sequence is shown as a broken circle, if you start zooming we need to automatically switch to showing a linear map.
When copying all or a subset of an aligned sequence, we now properly store the name of the aligned sequence on the clipboard.
Fixed various bugs with viewing alignments.
Fixed a bug where an enzyme name in brackets was not cleared when adding a 3' base to a blunt end or removing a 3' overhang.
Fixed a bug that prevented deselecting features in history view by Cmd/Ctrl + clicking.
Fixed numbers shown when mousing over bases right of "Original Sequence" in Sequence View while viewing an alignment.
Fixed a bug where after converting bases to upper or lower case, the change could sometimes revert after saving.
Fixed a bug with updating the selection in the alignment interface after editing the reference sequence.
After editing the reference sequence, expanded aligned sequences now remain expanded.
Fixed a bug that prevented copying or blasting feature run-on translation selections.
Fixed bugs with placing the cursor or making selections after edits were performed while using the "Edit DNA Ends" dialog.
Fixed a glitch that allowed content to be selected in the Keyboard Shortcuts and Gestures dialogs when right clicking.
"Align with Other Sequences..." now logs the last directory content was selected from and using that directory by default when aligning with additional sequences, or opening files in general.
Arrow heads are now shown correctly in Map View for sequences that align around the numerical origin.
SnapGene can now be activated and make network connections when sitting behind a proxy server that requires authentication.

New in SnapGene 2.1.1 (Nov 14, 2013)

New in SnapGene 2.1.0 (Sep 17, 2013)

New Functionality:
Gaps in alignments are now visible in Map View.
Added "Next/Previous Aligned Region" buttons for navigating an alignment in Sequence View.
Alignment controls can now be horizontally resized. (Suggested by Adrienne Luoma)
You can now customized the MW Markers menu (Suggested by Dan S.)
Added a "Show DNA Molecular Weight" Command. (Requested by Jeffrey Carey)
You can now export sequence selections directly to a file. (Requested by Alex Zelenskyy and Izhak Kehat)
Enhancements:
While scrolling past a large gap in an aligned sequence in Sequence View the sequence no longer disappears.
Enhanced automatic scrolling in response to clicking the "Next/Previous Discrepancy" buttons in Sequence View.
The navigation buttons while viewing an alignment in Sequence View can now be used to jump to non-aligned regions of the reference sequence.
Added a "Show/Hide Enzymes" command to the Enzymes menu for quickly toggling the display of enzymes in Sequence and Map Views.
Added various shortcuts for alignments to the "Keyboard Shortcuts" dialog.
Added a "Save Enzyme Set" button to Enzymes View.
Various optimizations that make aligning with multiples sequences faster as well as opening files that contain multiple embedded aligned sequences.
The Home and End keys can now be used to scroll vertical scroll areas.
Added "Oxford Genetics" to the list of predefined sequence authors.
Enhanced suggested file names when using "New File from Selection"
Matches within translations are no longer returned when performing a search while using Features View. (Suggested by Keoni Gandall)
Lowered the minimum PCR primer Tm to 45°C (Suggested by Keoni Gandall)
Added suggested tips and information to the toolbar in SnapGene Viewer.
Enhanced summary string when using Blast DNA for enzyme, and primer based selections.
Added the legend and fixed the pinch icon in the Gestures dialog on Windows.
Removed "Insect Cells" and "Plant Cells" from the "Natural DNA" menu in the description panel since natural DNA comes from specific species.
Sequence View now auto scrolls to selected aligned sequence after selecting a sequence using Map View.
Removed red pliancy and instead clicking anywhere on a features/primer in the import and detect common features dialogs now toggles importing the clicked item.
Enhanced detection of common features to allow for 1 bp omissions at either end of certain feature types.
When deleting/replacing the visible end of an aligned sequence, we now delete/replace the actual end of the aligned sequence if the end was not visible due to trimming.
Added controls for setting the default transformation strain to the "Edit Strains List" dialog.
The text edit within the New/Insert/Replace dialogs should now be far more responsive when working with and reverse complementing large sequences.
Various textual, icon, and alignment enhancements.
Bug Fixes:
Fixed hang on XP when OKing out of Edit Feature dialog on Windows XP while viewing a linear map. (Reported by Ayelet)
Fixed a regression in 2.0 that resulted in blunt restriction sites not being displayed at the end of Sequence View lines. (Reported by Lucas Almendra)
Fixed a bug where the Primers dialogs incorrectly reported the number of annealed bases when simplified primer-template duplexes are shown. (Reported by Devin Strickland)
Fixed a bug with properly displaying origin-spanning primers in the Primer dialogs. (Reported by Devin Strickland)
Fixed a bug that prevented pasting large copied selections (> 1 Mbp) into the New, Insert and Replace Bases dialogs. (Reported by Siddarth Arumugam)
Fixed a crash that could occur while detecting common features. (Reported by Jordan Ang)
Fixed brief flashes that could occur while horizontally scrolling sequence view while viewing alignments.
Fixed a bug that could result in a hang when loading XML encoded data.
Fixed bugs with pliancy in Features and Primers Views.
Fixed a bug where alignments mode was not turned off automatically when manually switching from a linear to a circular map representation.
Fixed a bug that prevented SnapGene from automatically detecting a software update is available.
Fixed a bug where when expanding an aligned sequence, viewing it as a double stranded sequence, the sequence would stop scrolling to the left once the last trimmed aligned base was visible.
Fixed the following bugs when viewing reverse aligned sequences as double stranded sequences: -Enzyme tooltips and sequence endpoint labels showed the incorrect cut position -Sequence endpoint labels were sometimes incorrectly shown when aligned sequence was trimmed or sequence end was not aligned. -Start/End labels should be swapped -Incorrect number shown at the right end
Fixed a small memory leak when changing the default MW markers.
Fixed bugs with setting the default MW markers
Fixed a glitch where items in the "Edit Strains List" dialog were selectable.
Fixed a hang that could occur while viewing zoomed maps with aligned sequences.
Fixed a crash that could occur while using the Mutagenesis dialog.
Fixed a bug that could result in trimmed trace data being displayed right of aligned called bases.
Fixed a bug where when undoing an edits to aligned sequences the trimmed range was not properly restored.
Fixed a bug where when editing an aligned sequence the length was not updated at the lower left when expanded within Sequence View.
Fixed bugs with automatically scrolling to aligned sequences.
Fixed a bug where a crash could occur while viewing an alignment.
Fixed a bug that could result in annotations being lost if the application crashed in the middle of saving out changes to a document.
Fixed a bug with restoring the trimmed range after undoing a deletion or replacement on an aligned sequence.
Fixed a bug that prevented inserting bases at the very end of a sequence trace or aligned sequence, or the very beginning of a reverse aligned sequence, or undoing a deletion or replacement that effectively requires an insertion at such a location.
Fixed a bug where after performing an insertion, deletion, or replacement on an aligned sequence, the view could scroll improperly.
Fixed a bug where if an aligned sequence that contains a selection was unchecked the view would scroll. Similarly, when undoing such an action the original selection is now restored.
Fixed a regression in 2.0 with properly displaying long fixed line widths that require horizontal scrolling in Sequence View.
Fixed a glitch where sometimes while interacting with Sequence View and viewing an alignment, content would stop expanding properly to use vertical space.
Fixed a bug where when viewing a wrap-around alignment the aligned sequence would never disappear while scrolling when not technically visible.
Fixed a bug that prevented properly scrolling to an aligned sequence that wraps around the numerical origin when selecting it in the list or using the "Next/Previous Aligned Sequence" buttons.
Fixed a potential crash while scrolling MSA mode and viewing an aligned sequence as a double stranded sequence.
Fixed a bug with displaying alignments that wrap around the numerical origin where no aligned region wraps around the origin.
Fixed a bug with displaying alignments after resetting the numerical origin, flipping the sequence, or undoing such actions.
Fixed a bug where while using a manipulation dialog if you closed a Noncutters dialog, then minimized and restored the manipulation dialog the Noncutters dialog would reappear.
Fixed various glitches where tapping enter while using the Add/Remove controls in Enzymes view did not respond as expected.
Page Up/Down now can be used to scroll Sequence View while viewing a multiple sequence alignment.
Added missing window resizing size grip from lower right corner of the Import Features/Primers and Detect Common Features dialogs.
Fixed a bug where if you made a DNA selection in Map View, then selected an aligned sequence, when switching to Sequence View the view auto scrolled to the DNA selection instead of the more recently selected aligned sequence.
Fixed a bug that could result in trace curve data being displayed beyond the end of an alignment.
Fixed various bugs with undoing deleting aligned sequence bases.
The Sequence View ruler no longer displays tick marks and number right of the last zoomed base.
Fixed glitches that could result in duplicated ancestors being stored within a file or in rare cases lost ancestors.
Fixed a potential bug where when saving out changes to file annotations non volatile data (e.g. DNA) could potentially be lost in the process.
Fixed a bug where when using the "Insert Fragment(s)" dialog if the insertion was the exact same size as the fragment to be replaced, features in the replaced ranged were not removed as they should be.
Fixed a bug where when inserting a flipped fragment that was already linearized the features in the insert were not flipped as they should be. (Reported by Pieter J deJong)

New in SnapGene 2.0.0 (Jul 24, 2013)

New in SnapGene 1.5.3 (May 9, 2013)

New in SnapGene 1.5.2 (Mar 16, 2013)

New in SnapGene 1.5.1 (Mar 2, 2013)

New Functionality:
SnapGene now supports network and floating licenses for institutions.
Enhancements:
Improved the default filename when printing to PDF from the "Noncutters", "Genetic Codes", and "License Agreement" dialogs.
You can now trigger the "Select Range" action using the menu shortcut when focus is in the find controls, zoom controls, or "Description Panel".
Added message indicating references can be imported from PubMed.
Updated standard common features database.
Various textual and font enhancements.
Bug Fixes:
Fixed glitches with showing pliancy for the map label when it is placed below a circular map.
Fixed glitches with displaying enzymes and primers in broken circular maps.
Fixed a glitch that prevented selecting an entire linear sequence when first clicking the "End" label and then shift clicking the "Start" label.
Fixed a bug where when clicking "Set Default Sequence Author…" the associated field did not automatically get focus when the Preferences dialog was shown.
Fixed a bug where the most recent enzyme name used to cleave the downstream end of a linear sequence was not cleared when a double stranded selection at the downstream end was removed.
Fixed a bug where when using the Insert Fragment(s) dialog, if you flipped a fragment, then deselected the insert in the fragment list, when reselected the flipped state was not reset in the overview to reflect the state in the side controls.
Fixed a bug where the "Import from GenBank" command could sometimes fail to download a sequence.
Fixed a memory leak that could result in a crash when a file that was once open in a closed manipulation dialog is deleted or renamed.
Fixed a bug that prevented displaying a context menu when right clicking on DNA or empty space while using sequence view in a manipulation dialog.
Fixed a bug that prevented pasting into the feature segment endpoints within the Make/Edit Feature dialogs. (Reported by David)
Fixed a bug that could result in the omission of the sequence length in circular maps.
Removed ORF information from feature tooltips when the feature uses an alternative start codon and includes a full coding sequence.
Fixed a bug where after auto completing a "Laboratory Host Organism" or "Source Organism" in the "Description Panel", the auto completed value was not saved.
Fixed a bug where when changing the "Source Organism" to "Escherichia coli" a dialog would appear multiple times asking if you wanted to change the methylation if no methyl groups were present.
Fixed a bug where when viewing a broken circle map the correct top strand length was not shown.

New in SnapGene 1.5.0 (Feb 19, 2013)

New Functionality:
SnapGene now supports simulating "Gibson Assembly"
SnapGene can now display estimated quality data for sequence trace files that lack quality data.
You can now view raw sequence trace data in .AB1 sequences.
SnapGene now supports viewing broken circular maps for linear sequences.
SnapGene now supports sharing feature segment endpoints and as result can properly display features that are effected by ribosomal slippage.
You can now export a simulated agarose gel as an image or fragment list.
Enhancements:
Improved non-linear vertical and horizontal scaling controls when viewing sequence traces.
Enhance sequence trace auto scaling.
When simulating InFusion Cloning or Gibson Assembly, you can now select a restriction site or fragment to indicate a site of insertion or a fragment to be amplified by PCR.
Improved default window placement and size.
Added a "If you have purchased SnapGene, click [here] to enter your new registration code." message to the "Your trial copy of SnapGene will soon be deactivated" dialog shown while a free trial is still active.
Updated references to "Fermentas" to indicate "Thermo Scientific"
Replaced the global default PCR polymerase setting with per-manipulation settings.
After choosing a template while using a manipulation dialog, focus is now transferred by default to embedded document.
Various color, textual and alignment enhancements.
Bug Fixes:
Fixed a bug that could result in a crash when detecting common features. (Reported by Dana Nadler)
Fixed a bug that prevented SnapGene from opening some SeqBuilder files. (Reported by Jason Signolet)
Fixed a bug where after opening a sequence trace SnapGene should default to that directory when opening future files.
Fixed a bug where when duplicating a lane in the Simulate Agarose Gel dialog, the template and chosen enzymes did not appear right away.
Fixed a bug that could result in a crash when simulating InFusion Cloning.
Fixed a bug where the Launch dialog was not hidden when the "New File", "Open", and "Import from GenBank" dialogs were first shown.
Fixed various bugs with importing GenBank, MacVector, and other files that include overlapping segments, aka features with ribosomal slippage.
Fixed a bug that allowed registration information to appear to be modified in the registration dialog via paste.
Fixed a bug with displaying translated reverse directional origin spanning features in circular maps. (e.g. lacZα in pGEM-T.dna)
Fixed a regression that broke "Anneal Oligos"
Fixed a crash that could occur when changing the font size before specifying the template for all tabs in a PCR based manipulation dialog.
Fixed a bug where when switching between similar type windows (e.g. DNA sequence windows, trace windows, cloning dialogs), the menu state (text and enabled/disabled state of actions) might reflect the state for the previously activate window sometimes.
Fixed a bug where on OS X after first activating SnapGene, actions within the SnapGene menu could be unresponsive until you quit and restart the application.
Fixed the font size and family shown in the "Getting Started" dialog as well as the button spacing and window margin.
Fixed a bug where when pasting into the "Product Name" control in a manipulation dialog did not updated the viewed product or effect the product generated when accepting out of the dialog.
Fixed a bug where the wrong fragment was amplified when using primers that overlap at their 3' ends.
Fixed various bugs where menus were not refreshed properly on Mac OS X when switching between windows.
Fixed a bug where the "Window -> Zoom" menu action was disabled on Mac OS OX.
Fixed a bug where when showing/hiding/erasing operations one or more levels down in history view the view would not refresh to reflect the change.
Fixed a bug where when using "Edit -> Cut" when a Feature selection, the underlying DNA should be deleted instead of removing he feature.
Fixed various bugs with finding enzymes.
Fixed a bug where when the find controls have focus the shortcuts for finding protein sequences and enzymes/features/primers failed to work.
Fixed various bugs with entering negative numbers while using the "Select Range" and "Go To" commands.

New in SnapGene 1.4.1 (Jan 24, 2013)

New Functionality:
SnapGene can now read sticky ends and features from SerialCloner files.
Added the ability to apply a segment color to all selected segments in the Make/Edit/Duplicate Feature dialogs.
Enhancements:
Added amino acid count and MW information to tooltip displayed when mousing over a feature segment.
When creating a new file from a selected feature, the default filename is now filtered to avoid including forbidding characters.
Stop codons are now highlighted in the Genetic Codes dialog as white on red.
Changed the shortcuts for "Nonredundant Commercial" and "All Commercial" enzymes to Opt+Cmd+A and Shift+Opt+Cmd+A respectively.
Improved detection of circular plasmids
Swapped the order of the two polymerase options. The default value for new installations is now "blunt".
Updated the common features database.
Various alignment, color, icon, and textual enhancements.
Bug Fixes:
Fixed brief yellow flash that would occur when launching manipulation dialogs. (Reported by Daniel Strongin)
Fixed a potential crash when editing primer names while using the PCR, Overlap Extension PCR, or InFusion Cloning dialogs. (Reported by Hilary B)
No longer automating associating .scf files with SnapGene on Windows to avoid conflicting with the "Minimize all Windows" and other shortcuts Windows provides via Shell Command Files. (Suggested by D. Allan Drummond)
Fixed various bugs with viewing and searching within trace files in the reverse orientation. (Reported by Erin Adams)
Fixed a bug where when editing custom common features their underlying DNA could change. (Reported by Klas Flärdh)
Fixed a bug where feature attributes became uneditable after splitting a segment. (Reported by Dana Nadler)
Fixed a bug that could prevent SnapGene from running on some Macs. (Reported by Justin Vrana)
Fixed a bug with inserting a fragment at a site that cuts at the origin of of vector. (Reported by Otakar Hlaváček) -Fixed a crash when printing Sequence View.
Fixed a bug that could result in slow downs on Windows when the default printer is inaccessible.
Fixed a bug where features view would not print content if it has not been viewed.
Fixed a bug where the feature tooltip could incorrectly indicate a feature has one more amino acids then is actually does when the translation begins in the 2nd or 3rd reading frame.
Fixed a bug that prevented changing the case of the map label.
Fixed various bugs that could result in the wrong file icon being shown in the title bar when viewing DNA sequences and sequence traces.
Fixed a bug that resulted in reverse directional features that wrap around the numerical origin not being displayed in circular maps.
Fixed bugs with inverting the selection within Features and Primers Views.
Fixed a bug that could prevent a valid in-frame fusion from being displayed properly in Sequence View when another feature is present.
Fixed a bug where after choosing a custom segment color the Make/Edit Feature dialog could become unresponsive.
Fixed a bug that prevented the list of common features from getting focus in the Common Features dialog.
Fixed a bug that prevented the default export format from being selected by default when exporting a map.
Fixed various bugs with inserting a fragment that is obtained by cutting a circular plasmid once.
Fixed a bug that resulted in a crash if SnapGene is unable to align with any specified files.
Fixed a bug where unsaved case changes were not retained when adding a feature to the list of custom common features.
Fixed various bugs with choosing the best feature to annotate when detecting common features.
Fixed a bug where various menu commands could incorrectly become disabled when switching tabs.
Fixed a bug where when hovering over a widget that spawns a tooltip instantly, after waiting ~10 seconds for the tooltip to disappear the application would crash on OS X.

New in SnapGene 1.4 (Dec 13, 2012)

New Functionality:
You can now scroll an entire sequence on one line in Sequence View.
SnapGene can now auto scale sequence trace data to correct for exponential decay.
SnapGene now supports just under 200 transformation strains.
You can now export specified feature data. (Suggest by Andy Crouse)
Primers can now be exported using a FASTA format (Suggested by Edward Wallace)
You can now copy feature and primer selections to the clipboard. (Suggest by Andy Crouse)
SnapGene now supports Retina displays on OS X.
Added preferences for the look and feel of sequence traces.
Enhancements:
When zooming, sequence view no longer attempts to avoid scrolling the content displayed and instead updates as expected. (Suggested by Devin Strickland)
Added "Check for Updates..." to bottom of help menu in launch dialog (Suggested by D. Allan Drummond)
Added URL's and buffer reactivity information for enzymes available from TaKaRa.
Updated the common features database
Opt/Alt+Delete can now be used to bypass warnings in all contexts, including deleting custom features while using Browse Common Features.
The Find controls while viewing sequence traces or aligning sequences are now hidden by default.
Substantially sped up opening and viewing files with large histories
When making a selection from within another view, or when using the Select Range command, Sequence View now attempts to scroll to display the entire range, not the last base (or in one case the 1st base).
When viewing large complex sequences, SnapGene should be more responsive while adjusting display options.
Optimized opening and interacting with sequences
By default only the first 5 rows of history are displayed by default for files with extensive history.
Changed keyboard shortcut for "Simulate Agarose Gel" from "Cmd+L" to "Shift+Cmd+G"
Enhanced the look and feel of the mismatching navigation buttons while using the "Align with Sequence Trace" command.
Enhanced positioning of the mouse position and drag indicators.
Enhanced the look and feel of various pull down menus on OS X.
Made "Delete X bp?", "Remove # Features?" and "Remove # Primers?" messages sheets on OS X.
Expired and incompatible licenses are now automatically updated at startup.
Now sending license information when reporting crashes to facilitate contacting users and resolving problems that are encountered.
Streamlined the look of primer binding sites in map view.
Various textual enhancements
Bug Fixes:
Fixed various bugs when working with sequences over 9999 bases in length on Windows using Brazilian Portuguese (reported by Gisele Picchi)
Fixed a bug that could result in crash when aligning sequences. (Reported by Marco Chiabudini)
Fixed a bug that could result in a crash when opening GenBank, MacVector and ApE files. (Reported by David Welkie)
Fixed issues with reading some FASTA, EditSeq, and GenBank files on and reading and writing custom enzymes sets on Windows. (Reported by Sidney Morris Jr)
Fixed a bug that could cause horizontal scrolling of sequence view to be sluggish, especially on computers with Retina displays. (Reported by Devin Strickland)
Fixed a bug where if the first primer used for PCR binds to the bottom strand and the second primer binds to the top strand, the melting temperatures for the two primers were swapped in the primer controls in the PCR and other PCR based manipulation windows. (Reported by Dan Kraut)
Fixed a bug where if two primers are selected the result in a full sequence selection, tapping the delete key should offer to delete the primers, not replace the selected bases.
SnapGene now properly checks for and requires a minimum version of OS X (SnapGene now requires 10.5 or later)
Fixed a bug where "Primers" and other buttons in History View could shift or disappear after minimizing and restoring the window.
Fixed a bug where when a sheet was displayed, hiding and restoring the window could cause the sheet to turn blank or disconnect from the window.
Fixed a bug that could result in a crash when replicating feature regions when extending a sequence by linearizing with a sticky cutter or using partially overlapping primers to amplify a fragment.
Fixed a bug where when viewing incredibly large sequence (hundreds of millions of bases) with all enzymes displayed at the largest font size and a narrow window width it was impossible to scroll in sequence view.
Fixed various glitches with finding enzymes, features and primers.
Fixed a bug that could cause SnapGene to crash when toggling enzymes, features, primers, or changing display options in other ways while not viewing map view.
Fixed a bug where the Launch dialog would not reappear on Windows after canceling out of the "New DNA File" or "Import from GenBank" dialogs.
Fixed a bug where the "Quit" menu action could become disabled on OS X.
Fixed placement of "Show History" buttons below linear maps in history view.
Fixed a bug where if you transferred focus away from SnapGene using Alt/Cmd+Tab, then moved the mouse and transferred focus back to SnapGene, the ruler in sequence view did not properly show where the mouse until it moved again.
Fixed a bug that could result in a crash when selecting a non native file while using the Align with Trace, Mutagenesis, or Add Primer dialogs.
Fixed a bug where when using the "Select Range" and "Go To" commands the dialog incorrectly indicated the last base in the pull down menu and allowed entering values one greater then the actual sequence length or visible range.
Flipping a trace sequence is no longer an undoable action since it really is an unsaved viewing option. In so doing SnapGene no longer informs you the sequence is modified and asks to save changes before closing if all you have done is flip the trace sequence.
SnapGene now refuses to open files that contain no DNA segment or an empty DNA segment (e.g. that SSpa file sent to us by a user. SnapGene could crash later while open if it actually tried to navigate such a file).
Fixed a bug with opening or aligning to extremely degenerate DNA sequences.
Fixed a bug that allowed scrolling short sequence traces that should not require scrolling.
Fixed a bug where when using "Sort Feature List", a blank option was listed in each pull down menu.
Fixed a bug where when using "Sort Primer List", if you expanded the dialog to show all options a blank entry was listed at the bottom.
Fixed a bug that could result in a crash when closing a tabbed manipulation dialog.
Fixed a bug that could cause a crash when checking to see if a plasmid map name is under the mouse.
Fixed a bug that could cause SnapGene to crash when importing some files.
Fixed a bug that could result in a crash when quitting the application.
Fixed a bug that could result in a crash while using the Common Features dialog.
Fixed various bugs that could result in a crash when detecting an open file is moved or deleted.
Fixed a crash that could occur when using the keyboard to modify the selection while using Features or Primers views.
Fixed problems that could occur when exporting primers to a list if a primer name contains the chosen delimiter.
Fixed a bug where N's were copied as -'s for sequence trace selections.
Fixed a bug where a map label should not show pliancy until the window has focus.
Fixed a bug where in history view if the current sequence or an ancestor contained one or more periods in its name the part of the name could be omitted.
Fixed a crash that could occur when opening new files and checking for map name pliancy for a map was generated.
Fixed a bug where Save As from a trace window would not default to the proper directory.
Fixed glitches with document icons on OS X.
Fixed glitches with pull down menus on OS X.
Fixed a bug where when completely zoomed out some enzymes would incorrectly indicate that there are "No sites within the zoomed range".
Fixed a bug that could result in a crash when performing an alignment.
Fixed a bug with creating feature segments downstream of a feature gap.
Fixed a bug with updating feature translations when editing a feature with one or more introns.

New in SnapGene 1.3.3 (Oct 26, 2012)

New in SnapGene 1.3.2 (Oct 19, 2012)

New in SnapGene 1.3.1 (Sep 20, 2012)

New in SnapGene 1.3 (Aug 24, 2012)

New Functionality:
SnapGene can now open Clone Manager .cm5 files.
SnapGene can now open FASTA archives. The FASTA importer has also been improved to decode sequences descriptions and accession numbers.
SnapGene now simplifies the display of complex primer-template duplex loops. Accurate melting temperatures are still based on the most energetically favorable duplex structures. If you would like to view the full structures you can restore this behavior under Preferences -> Primers.
SnapGene now automatically flips fragments when performing InFusion™ Cloning and Overlap Extension PCR. In addition, SnapGene will now automatically choose the appropriate primers to amplify the fused product when performing Overlap Extension PCR.
You can now export either rich or simplified GenBank files, the latter of which lack color, directionality, cleavage arrows and segment information.
You can now import primers from Vector NTI .oa4 oligo archives and FASTA sequences and archives.
Enhancements:
You can now align to multiple sequence files at once using the renamed View -> "Align with Sequence Traces" command.
Improved automatic hyperlink creation when importing from other file formats.
Improved opening GenBank files exported from Clone Manager.
Dramatically speed up refreshing Map and Enzymes Views when thousands of features or N-stretches are visible.
Sped up opening multiple files.
Improved display of discrepancies and poorly called bases while viewing alignments.
Improved display of primer length, melting temperature, and number of binding sites while using the PCR, Overlap Extension PCR, and InFusion Cloning dialogs.
Enhanced the new version available dialog to display screenshots and descriptive text that summarizes the major functionality in a newer version.
Improved the behavior when finding enzymes, features and primers within Sequence and Map views.
In addition to A, G, and R, you can now also add a single C, T, and Y while using the Edit DNA Ends dialog.
Updated the common features database to over 317 unique standard common features.
Added NEB's "1 Kb Extend DNA Ladder"
Added "Agilent Technologies" and "MoBiTec" to the sequence author menu in the Description Panel.
When exporting a map for the 2nd time, the default format is now the last format used.
You can now upgrade from a free trial to the paid version before your free trial expires by using a new "Enter New Registration Code" button in the registration dialog.
On OSX the launch dialog now returns when all windows are closed. If you would like to restore the previous behavior (where once closed the launch dialog does not return) you can uncheck this option under Preferences -> General
Enhanced the Windows installer to check for running copies of SnapGene during installation. If present you now get a chance to quit them before proceeding with installation instead of getting error messages about being unable to install various files.
Now displaying more descriptive error message if unable to contact the server or some other error takes place while activating, importing from GenBank, fetching a reference from PubMed, etc.
Removed alarming yellow template is already linear message when performing InFusion™ Cloning with a template that is already linear.
Various alignment enhancements.
Bug Fixes:
Fixed various glitches that could occur when attempting to create/save files with filenames that contain invalid characters.
Fixed various bugs with the "Browse..." action in the Simulate Agarose Gel and PCR dialog's template menu.
Fixed various bugs with auto-completing enzyme names while using the Simulate Agarose Gel, cloning, and other manipulation dialogs.
You can now use File -> Print from the Simulate Agarose Gel dialog.
Fixed a bug where the jump to the previous/next mismatch buttons in the Align dialog would not always work.
Fixed various bugs with the Select Range and Go To commands while using the Align dialog when the alignment wraps around the numerical origin.
You can now use Cmd+W to close all modeless dialogs (e.g. the launch dialog) on Mac OS X.
Fixed a bug where when importing features from another file it was possible to end up with duplicate copies if a given feature is present more then once in the target sequence.
Fixed a bug with saving modifications to the sequence author.
Fixed a bug with highlighting the appropriate strand when displaying DNA matches that partially overlap a sticky end.
Fixed a bug with activating a copy of SnapGene when an older outdated or expired license is already present on a Windows system.
Various other software license improvements and bug fixes.
Fixed a bug that could result in the wrong primer being replaced or the application to crash when editing a primer and renaming it to replace another primer.
Fixed a reported crash when using the insert symbol dialog.
Fixed a bug where not all sequences were always imported when opening Vector NTI .ma4 archives. (Reported by Tomas Bos)
Fixed various bugs with painting Enzymes View's mini-map ruler.
Fixed a bug where after browsing to choose a file to import primers from, that file was not added to and listed in the recent primer lists pull down menu when using the import primers form a list dialog again in the future.
Fixed a bug with displaying bottom bound primers that have multiple overlapping non-hybridized regions.
Fixed a bug where after using Select All to select all primers within Primers view, it was usually impossible to deselect individual primers using Cmd+Click.
Fixed a bug where when using the InFusion Cloning -> Insert One Fragment dialog it was not listed as an open window. On Windows the Launch dialog could also be shown on top.
Fixed a bug where when a linear template is chosen, selecting an enzyme site would automatically check the "Linearize with restriction enzymes" option even though it was disabled.
Fixed a bug with transferring features when amplifying fragments that could result in features being replicated.
Fixed various bugs with decoding content from rich text (.rtf) encoded files.