What's new in Unipro UGENE 1.24.1
Sep 2, 2016
- A patch release that contains several major bug fixes
New in Unipro UGENE 1.24.0 (Aug 11, 2016)
- Workflow Designer:
- New element: “Convert SnpEff Variations to Annotations”. Element converts variations with SnpEff information into standard annotations, so you can observe them in the Sequence View.
- NGS workflows improvements.
- Bug fixes.
New in Unipro UGENE 1.23.0 (Jun 27, 2016)
- Auto-update: there is no need to download a new version manually anymore. As soon as the new version released, UGENE will ask your permission to update and with your consent the program will be updated automatically.
- Minor interface improvements and bug fixes.
- Performance:
- Opening of large Genbank files was improved.
- The visualisation of restriction sites was improved.
New in Unipro UGENE 1.22.0 (Jun 14, 2016)
- In silico PCR: Degenerate primers were supported.
- NGS: Extracting of an assembly region in BAM/SAM/UGENE database formats was supported.
- Sequence View:
- Annotations editing was improved.
- Configuration of translation frames visibility was simplified.
New in Unipro UGENE 1.16.2 (May 22, 2015)
- A patch release that contains several major bug fixes and minor interface improvements requested by users
New in Unipro UGENE 1.16.1 (Mar 18, 2015)
- A patch release that contains several major bug fixes and minor interface improvements requested by users
New in Unipro UGENE 1.16.0 (Feb 21, 2015)
- Important changes in this major release include:
- Advanced and comfortable search in a project
- Usability:
- Sequence Viewer resizing
- Regrouping of the Tools menu items
- Workflow Designer: generating of output file names
- Sanger reads quality control and alignment
- NGS:
- Reads quality control with FastQC
- Variations annotation with SnpEff
- Alignment Viewer: conservation level highlighting
- Vector NTI sequence format
New in Unipro UGENE 1.15.1 (Dec 29, 2014)
- This is a patch release that contains several major bug fixes and minor interface improvements requested by users:
- Bug UGENE-3900: Disappeared selection in chromatogram view
- Bug UGENE-3896: Several small problems with Project View
- Bug UGENE-3894: Problem opening trees created from some alignments
- Bug UGENE-3886: Extract MSA consensus wizard crash
- Improvement UGENE-3868: Vector NTI GenBank format: support labels
- Sub-task UGENE-3850: UGENE-3841 SAFE_POINT triggers on creating annotations from find results loaded from file
- Bug UGENE-3835: Circular view draw huge annotations incorrectly
- Bug UGENE-3834: Annotations that intersect a junction point are drown over each other in Circular View
- Bug UGENE-3833: Relations are broken when sequence is renamed
- Bug UGENE-3829: DAS annotating crash
- Bug UGENE-3824: BWA-MEM status on Windows is not clear
- Bug UGENE-3823: Verify tests for raw NGS worfklow samples
- Bug UGENE-3822: Shared database can not be initialized
- Bug UGENE-3821: Error message in Primer3 search should contain more information
- Bug UGENE-3819: Reads for assembly in a shared database are not drawn
- Improvement UGENE-3818: Common wizard of the raw RNA-seq data processing workflow sample
- Bug UGENE-3817: The "Region" combobox switches incorrectly in the Find Pattern OP tab
- Bug UGENE-3816: UGENE fails on a phy tree file opening
- Bug UGENE-3815: SAFE_POINT on a short sequence translation export
- Bug UGENE-3813: UGENE crashes on auto-annotating
- Bug UGENE-3812: UGENE crashes on setting new sequence origin
- Bug UGENE-3809: UGENE crashes on opening chromatogram
- Improvement UGENE-3805: Creating reverse and complement sequence in the Sequence View
- Bug UGENE-3788: Incorrect annotation handling on the sequence crop
- Bug UGENE-3780: Selection marks unexpectedly disappear on the Chromatogram view
- Bug UGENE-3779: Zoom in assembly view works incorrectly
- Bug UGENE-3778: Circular view cannot be exported as image
- Bug UGENE-3767: Fix tab order on the Find Pattern widget
- Bug UGENE-3762: "Delete selected annotations" action works wrong
- Bug UGENE-3757: UGENE crashes on opening PDB
- Bug UGENE-3753: Renaming of objects exported from the DB hangs UGENE
- Bug UGENE-3749: Incorrect right click processing in MSA Editor
- Bug UGENE-3738: CAP3 result file cannot be opened in Assembly Browser
- Sub-task UGENE-3736: UGENE-3841 Find pattern with regexp doesn't allow to find patterns like "A{4,6}"
- Bug UGENE-3733: files in .ace format are not imported to database
- Improvement UGENE-3728: Fix shared object order in the Project View
- Bug UGENE-3718: Tophat: wrong Bowtie path is detected
- Bug UGENE-3669: Some cistrome and tuxedo tools throw errors
- Bug UGENE-3668: Bad layout in cistrome wizard
- Bug UGENE-3643: Wrong behavior of database tree selector
- Improvement UGENE-3618: Find patter widget: "Use pattern name" option change shouldn't run a new find task
- Bug UGENE-3459: Descriptions and versions of external tools
- Improvement UGENE-3449: Add "Edit annotation" item to menus
- Improvement UGENE-3390: Annotation regions order unification
- Bug UGENE-3359: Peaks on a chromatogram are shifted
- Bug UGENE-3342: Dotplot view can't be closed
- Improvement UGENE-3221: Limit 15 bases for length of pattern name
- New Feature UGENE-2938: Drag'n'drop documents
- Improvement UGENE-2633: Copy/paste in Crash Reporter window
- Bug UGENE-2510: Fix the MAFFT task progress
- Improvement UGENE-2004: External tools settings should be saved on the preferences closing.
- Improvement UGENE-1505: Get sequence by annotation: add region in source sequence in result names
New in Unipro UGENE 1.15.0 (Dec 2, 2014)
- IMPORTANT CHANGES IN THIS MAJOR RELEASE INCLUDE:
- Quick search in a sequence without creation of annotations
- PCR in silico
- NGS:
- Spades de novo assembler
- Export of a short reads assembly coverage
- Raw NGS filtering workflow samples
- Circular View and circular sequences:
- Support of all algorithms for circular sequences: ORF, restriction sites, BLAST, etc.
- Circular View visualisation settings
- Shared database:
- Support of shared databases in the UGENE Workflow Designer
- Usability improvements:
- Welcome page
- Remembering of Options Panel setting within one
New in Unipro UGENE 1.14.2 (Oct 8, 2014)
- Contains several major bug fixes and minor interface improvements requested by users.
New in Unipro UGENE 1.14.1 (Sep 10, 2014)
- Help system:
- Help buttons were added into all UGENE dialogs.
- The documentation was moved to the Atlassian Confluence system, this makes it easier to search for required information in it.
- Shared storage: sharing of bioinformatics data in a lab. For details, see this page.
- Alignment Editor:
- Overview for a multiple alignment was added, a lot of configuration options are available.
- A multiple alignment consensus can now be exported.
- Phylogenetic Trees:
- PhyML Maximum Likelihood was integrated.
- It is now possible to re-root a tree.
- Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
- Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
- Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)
- NGS:
- BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
- Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
- UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
- A splash screen was added on the UGENE startup.
New in Unipro UGENE 1.14.0 (Aug 1, 2014)
- Help system:
- Help buttons were added into all UGENE dialogs.
- The documentation was moved to the Atlassian Confluence system, this makes it easier to search for required information in it.
- Alignment Editor:
- Overview for a multiple alignment was added, a lot of configuration options are available.
- A multiple alignment consensus can now be exported.
- Phylogenetic Trees:
- PhyML Maximum Likelihood was integrated.
- It is now possible to re-root a tree.
- NGS:
- BWA-MEM tool for aligning short reads was integrated. The tool is available in the GUI dialog and in the Workflow Designer.
- Different workflow elements for sorting, merging and filtering and trimming of NGS data were added (BAM and FASTQ files).
- Shared storage: sharing of bioinformatics data in a lab.
- Circular View and circular sequences: a possibility to mark a nucleotide sequence as circular was added. This mark affects how a pattern is searched in the sequence – results located over the end-start junction of it are also found.
- Plasmid features: auto-annotation of the plasmid features like promoters, regulatory regions, primers, etc.
- Export images: exporting of images was improved (multiple alignments, circular molecules, etc.)
- UGENE Public Storage: the storage can be remotely accessed from any UGENE instance. It contains common genomes and hundreds of plasmids.
- A splash screen was added on the UGENE startup.
New in Unipro UGENE 1.13.3 (Jun 6, 2014)
- Contains several fixes and improvements of the remote NCBI BLAST feature in UGENE and a fix of an error with several UGENE bundles on Mac OS X.
New in Unipro UGENE 1.10.0 (Dec 10, 2011)
- New tools: MrBayes, BWA (all platforms), update of Bowtie and BLAST tools
- Short reads assembly viewer: performance and reads coloring improvements
- Work with large data sets: open, view and annotate huge DNA files on a usual desktop
- Workflow designer: new data filtering elements
- Sequence viewer: new DNA flexibility and GC Frame Plot graphs
- All in one package: download UGENE, documentation and external tools in a single file!
New in Unipro UGENE 1.9.8 (Oct 27, 2011)
- Fixed a crash during short reads export from the Assembly Browser
- Fixed a crash when using PsiPred package with some special data sets
- The ORF Marker now correctly processes boundaries of circular sequences
- Support of the BAM and GFF formats was improved
- Chinese translations were improved
New in Unipro UGENE 1.9.6 (Aug 23, 2011)
- Association between annotations and sequences in project files is restored
- Assembly Browser doesn't hang anymore on loading results from alignment algorithm
- Reverse-complementary sequences from results of CAP3 algorithm are visualized
- correctly
- MultiFASTA files can be opened as merged sequences
New in Unipro UGENE 1.9.5 (Aug 18, 2011)
- Fixed reported crashes with ORF auto-annotations
- Assembly Browser: better & faster coverage
- Integrated new tool: CAP3
- New plugin: DNA flexibility
- Check bug tracker for details.
New in Unipro UGENE 1.9.4 (Jul 13, 2011)
- New features, improvements, bug fixes:
- Fixed reported crashes with ORF auto-annotations
- Assembly Browser: better & faster coverage
- Integrated new tool: CAP3
- New plugin: DNA flexibility
- Check bug tracker for details.
New in Unipro UGENE 1.9.2 (Mar 25, 2011)
- Additional info: support for universal package is dropped. From now, only win
- x86 package is supported
New in Unipro UGENE 1.9.1 (Feb 15, 2011)
- Circular view: zooming added
- Export of rev-comple annotations fixed
- MSA dialogs: GUI fixes
- Enzymes: fixed search in range option
- Workflow Designer: fixed workers promts
- Workflow Designer: openning schema with no meta info fixed
- Worfklow Designer: added ordering to element options
- Workflow Designer: added element "Retrive data from remote DB"
- Query Designer: added strand direction parameter to queries
- Supported pDRAW document format
- Added option to export group of annotations or annotation table to CSV
- KAlign crach fixed on amino MSA
- Cloning in silico: added option to edit fragments
- Cloning in silico: added option to annotate new fragments
- Cloning in silico: fixed incorrect ligation
- and more minor bugfixes.
New in Unipro UGENE 1.7.0 (Jun 1, 2010)
- New features & plugins:
- Major renaming: congene -> ugene, ugene -> ugeneui
- New plugin: genome aligner;
- New plugin: bowtie;
- Dna assembly to reference functionality added;
- Poistion-weight matrix advanced support added;
- MSAEditor: new zooming mode added;
- Circular view improved.
- Overview added to Sequence View;
- Integration with JASPAR and UniProbe.
- Alignment logo added.
- Command line interface improved.
- Command line version Workflow designer support added.
- Remote request re-worked.
- Scripting framework introduced in CSV import.
- Tree viewer re-worked, new modes added.
New in Unipro UGENE 1.6.0 (Jan 25, 2010)
- New plugins:
- Phylip plugin for building phylogenetic trees. Based on original Phylip 3.6 package:
- Neighbor Joining algorithm;
- Phylogenetic trees visualization;
- Integration with Multiple Alignment Editor.
- Distributed computing in UGENE:
- Support for launching HMMER 3 , Smith-Waterman , MUSCLE tasks on remote machines.
- Remote tasks support;
- New features and bug fixes:
- Search for tandem repeats introduced in Repeat Finder plugin;
- Project files transferability support;
- "Export project" feature;
- Interaction with remote databases: NCBI, PDB, Swiss Prot;
- BioStruct3D plugin: anaglyph stereo mode;
- and a lot more...
New in Unipro UGENE 1.5.2 (Sep 23, 2009)
- New plugins:
- MUSCLE 4 - a port of the newest tool for multiple sequence alignment by Robert C. Edgar;
- CUDA Support - an utility plugin which makes possible using NVIDIA graphical processing units for accelerating computational algorithms (Windows only).
- New features and bug fixes:
- CUDA-accelerated Smith-Waterman algorithm is ready to use for Windows users;
- The one of the most awaited features: sequence editing has been added;
- Primer 3 integration has been finished - a complete set of preferences is available now;
- Exporting annotation tables to CSV has been provided;
- New workers have been added to Workflow Designer: Sequence splitter and Remote request;
- Collecting statistical reports feature has been added. See the dialog on the first launch of v1.5.2;
- HMM2 models support has been added to HMM3;
- Filtering by hits number has been added to enzymes search;
- Now UGENE drops 'fantom' documents on project closing;
- Bug with incorrect handling of sequence range selectors has been fixed in SSP dialog;
- SSP algorithms, Primer3 and PDB parser now work correctly when launched in parallel;
- A serious bug affecting Fedora users has been fixed in PSIPRED.
New in Unipro UGENE 1.5.1 (Aug 1, 2009)
- New plugins:
- BALL - adds new types of molecular surfaces to UGENE 3D viewer
- New features and bug fixes:
- New feature: sequence line view and MSA editor now support saving fancy screenshots
- Congene crash on windows has been fixed
- HMM3 crash with malformed models has been fixed
- Crash with simultaneous primer3 tasks has been fixed
- Remote request is now stable when launched on Linux systems
- Missing Smith-Waterman search is restored
- Primer3 tasks now support cancelling
- Choosing selection color has been added to 3D viewer
- Sequence selection in Detailed View has been fixed a bit
New in Unipro UGENE 1.4.1 (Mar 25, 2009)
- Color schemes support in Alignment editor
- A camera lock option for multiple 3D protein models
- Sequence viewer optimized to be used with large amount of annotations (up to 1 million)
- Sequence viewer can show qualifier values instead of annotation names now
- Chromatogram viewer: quality values are now shown by default for ABIF files
- Several stabiliity and compatibility issues fixed in BLAST, MUSCLE and HMMER modules
- A number of minor stability fixes
New in Unipro UGENE 1.4.0 (Mar 11, 2009)
- New features:
- New plugin: Smith-Waterman. A complete implementation of Smith-Waterman algorithm
- New plugin: Restriction Enzymes. Marks restriction enzymes in a sequence. Supports 'bairoch' file format provided by REBASE database
- New plugin: Repeats Finder. Searches direct and invert repeats in DNA sequences. Optimized for huge sequences
- New plugin: DNA Statistics. Exportable statistical reports
- Workflow Designer: runtime state visualization of executed schema
- Workflow Designer: integrated support of workflow samples
- Workflow Designer: resizable items + snap to grid, customizable colors and fonts.
- MSA Editor: show non-gapped offsets for each sequence in alignment
- MSA Editor: a tool to search patterns in alignment
- Sequence view: support scale locks and synchronization for different sequences
- Sequence view: support for arbitrary number of rulers created by user
- BioStruct3D viewer: export of 3D PDB and MMDB models into 2D vector format (SVG)
- BioStruct3D viewer: a fast and extensible way to link active 3D model to Web resources
- Project view: supports 3 different view mode: grouping data objects by type, by document and flat view
- Project view: list of data objects for unloaded documents is shown
- Performance: UGENE now allows to specify ideal count of CPUs, threads and memory to be used
- DNA Export plugin: export of arbitrary multiple sequence alignments to FASTA format
- New file formats supported: FASTQ, MMDB (plain text ASN)
- Support for large (> 10Gb) files indexing for a fast data access
- Custom application GUI themes supported. Windows version of UGENE uses Office GUI theme by default.
- Improvements & bugfixes:
- MUSCLE plugin: part of the original algorithm was optimized to utilize multicore CPUs.
- HMMER plugin: SSE2 implementation of the algorithm was added;
- HMMER plugin: hmmsearch now works in parallel mode for a single sequence by default (gives >30x boost for quad-core CPU when used with SSE2)
- SITECON plugin: >50 new prokaryotic profiles to recognize transcription factor binding sites added
- Most the views and dialogs got performance and usability improvements
- Workflow Designer: now preserves additional info of processed data (like accessions, source etc) throughout overall computation.
- Workflow Designer: write tasks now provide controls to override existing target file (either overwrite, append or rename).
- Project view: supports relocation and copying of documents.
- Annotation creation: new annotations now can be added to an unloaded annotation table object. The object is automatically loaded in this case.
- MSA Editor: allows to change fonts, initial and limited support for zooming operations
- BioStruct3D viewer: support for single structure with multiple 3d models