Notes fo later releases.

Release Notes for Genome Workbench 2.12.10 (August 20, 2018)

New Features

• Graphical Sequence View: created category for proteomics tracks

Bug Fixes and Improvements

• Fixed some memory consumption issues
• Fixed hang up and freeze when loading project items first time on cold cache
• Graphical Sequence View: fixed display of alignments when local (non GenBank) molecule was BLASTed with NCBI database
• Graphical Sequence View: fixed errors in CDS tooltip (incorrect product sequence)
• Graphical Sequence View: fixed display of variation features imported from a GFF file
• Graphical Sequence View: fixed issues with HMM alignment tooltips and variants features
• Graphical Sequence View: fixed issues with rendering of short introns
• Graphical Sequence View: improved consistency of visual range synchronization options
• BAM/VDB format compatibility: fixed critical errors and crashes
• BAM file format: improved user interface and chromosome names re-mapping logic to be better compatible with NCBI molecule accessions
• Multiple Sequence Alignment View: fixed bug with garbled labeling of projected proteins
• File Import: fixed regression when input file is zip compressed
• File Import: improved with more common file extensions

Release Notes for Genome Workbench 2.12.8 (February 14, 2018)

New Features

• BAM Files: added WIG export for coverage graph

Bug Fixes and Improvements

• Text View: fixed crash showing GenBank format
• Text View: improved FASTA format view GUI (context menu) added “Expand All” option
• Graphical Sequence View: fixed disappearance of gene container of tracks on project update
• Graphical Sequence View: fixed crash when moving views (also applies to Multiple Sequence Alignment View)
• Graphical Sequence View: fixed various rendering issues for BAM alignments
• Graphical Sequence View: fixed issues last base not shown when zoomed in
• Graphical Sequence View: improved rendering of internal unaligned regions, showing the dashed line and number of unaligned bases
• Graphical Sequence View: improved info and help usability
• Graphical Sequence View: fixed crash in tooltips when clicked on unaligned base
• Graphical Sequence View: fixed crash on assembly/chr open-close scenario
• Multiple Alignment View: improved consensus rendering speed
• Reworked registry update mechanism for better stability
• Search View: fixed crash when selecting from results
• Tree View: fixed crash in Force layout mode
• Tree View: fixed rendering bug when colored selection set disappeared after subtree deletion
• FASTA Loader: improved handling of local ids
• GTF/GFF import: fixed various errors and conflicts in format readers
• Open View Dialog: improved to remember width of columns
• File Open Dialog: better format file names when adding to project to better reflect name and the type of bio-object
• Export: improved usability to automatically open the target folder, so user can quickly find the exported file
• Export: added warning if system is about to overwrite a file
• Installer: removed confusing settings for network PROXY environment, use automatic detection when possible
• Removed workspaces from the GUI as a non-essential concept
• BAM format: improved restore/removal of BAM data loader module on project close/re-open
• Fixed crash in situations when Genome Workbench home folder got accidentally deleted from disk
• Fixed bug in Windows OS version reporting
• Linux: fixed shutdown message typo

Release Notes for Genome Workbench 2.12.5 (September 18, 2017)

New Features

• BAM Files: added WIG export for coverage graph
• Text View: FASTA mode – implemented sequence selector
• Graphical Sequence View: new navigation tutorial
• Open Dialog: implemented logic to recognize and load Genome Assembly Accessions as GenBank accessions

Bug Fixes and Improvements

• MacOS-X: fixed crash with PDF editing
• ProSplign tool: fixed issues with local sequences
• Graphical Sequence View: performance optimizations of BAM data tracks
• Graphical Sequence View: fixes in selection mechanism when switching between different views
• Graphical Sequence View: matching (identical) bases in alignments now rendered clearer
• Graphical Sequence View: fixed broken links on SNP tooltips
• Graphical Sequence View: fixed incorrect display of nucleotide to protein alignments
• Graphical Sequence View: improved tooltips for non-coding genes, removed incorrect links
• Graphical Sequence View: fixed inconsistent display of identical bases with linked-mate pairs
• FASTA export of pairwise alignments improved not to produce multiple copies of alignments
• FASTA import: improved import of organism information
• Improved display of SRA files pointing to local sequences (de-novo assemblies)
• Search View: fixed component search incorrect display in Graphical Sequence View
• Tree View: fixed issues with sometimes missing labels
• Tree View: improved collapse of nodes
• Tree View: fixed issue in collapse nodes in Slanted Cladogram layout
• Multiple Alignment Viewer: fixed potential feature duplication
• GTF file format: fixed crash and other export issues
• ORF finder: fixes in length calculations
• MacOS: fixed automatic loading of project files (*.gbp) on double click
• Generic Table View: improved clipboard copy of selected column
• Fixed descriptions of Alignment Summary View and Multi-Pane Cross Alignment View

Release Notes for Genome Workbench 2.12.0 (June 22, 2017)

New Features

• Integrated new popular Multiple Alignment tools: KAlign, MAFFT, Clustal Omega
• Export of Multiple Alignments in FASTA Alignment format, compatible with third party tools and viewers
• New reworked FASTA import for sequences and alignments
• BAM files: project interface now allows sequential adding multiple BAM files or SRA accessions to view side by side in Graphical Sequence View
• Open Dialog: can now open files via HTTP and FTP protocols
• Open Dialog: it is now possible to add NA (annotation submitted to NCBI) to the project and then open Text View on that NA to inspect the content

Bug Fixes and Improvements

• Graphical Sequence View: improved track handling, fixed major issues with unexpected track appearance/disappearance, fixed issues with saving tracks and options over the restart
• Graphical Sequence View: fixed crash in tooltips at max zoom for NG alignments with propagated features
• Graphical Sequence View: fixed processing of histogram settings
• Graphical Sequence View: improved opening/initialization time
• Graphical Sequence View: fixed false mismatch issues in alignments
• Graphical Sequence View: improved BAM pileup graph rendering
• Graphical Sequence View: improved label for non-gene features (regulatory, protein_bind, misc_feature, repeat_region, and a few others)
• Graphical Sequence View: fixed discrepancies in graphs RNA exon coverage
• Multiple Alignment View: fixed hang if alignment referred to some unknown molecule
• Multiple Alignment View: improved compact mode not to show titles for groups of tracks
• Gene Model Tool: fixed crash
• Tree Viewer: fixed crash with zooming in circular layout
• Tree Viewer: improved rendering of collapsed subtrees, made it more visible
• Improved performance and usage statistics collection to provide better quality of service
• Fixed issue with intermittent incorrect validation of molecule ids (required restart of the program to restore the function)
• Fixe issues with GFF import
• BAM files: fixed issues related to BAM import, when no reference sequence was selected for adding into the project
• BAM files: added option to filter sequences on load
• Project Tree View: improved handling of non-actionable menu items (disabled when not handled)
• Dot Matrix View: fixed issues with selection broadcasting processing
• Search View: ORF search – fixed incorrect tooltips
• MacOS: improved crash detection and handling

Release Notes for Genome Workbench 2.11.10 (March 10, 2017)

New Features

• Critical improvement in HTTPs protocol communication with NCBI
• Graphical Sequence View: improved track configuration dialog, improved classification, search, more tracks are now available
• New manual for search in bio-trees
• Multiple Alignment View: implemented new coloring scheme: conservation

Bug Fixes and Improvements

• MacOS: fixed issues with downloading and using masking files
• Multiple Alignment View: fixed a crash
• Graphical Sequence View: fixed crash in zooming to some areas
• Graphical Sequence View: fixed issues with tracks disappearing
• Graphical Sequence View: corrected sequence for projected features found on protein to DNA alignment
• Graphical Sequence View: fixed “Go to sequence” dialog on MacOS
• Graphical Sequence View: performance improvements for displaying large alignments
• Graphical Sequence View: improved initialization time when opening a second instance
• Graphical Sequence View: improved the display default to link mate pairs
• Graphical Sequence View: fixed cosmetic issue in grayscale mode
• Tree View: fixed issues with not displaying tooltips
• Tree View: improved work with collapsed nodes/sub-trees
• Tree View: performance optimizations for Force Layout
• Multiple Alignment View: fixed logic in tooltips
• Improved cache management
• Fixed crash when user removes Active Object Inspector
• MacOS: fixed issues with windows floating on top of some dialogs

Release Notes for Genome Workbench 2.11.7 (December 29, 2016)

New Features

• Critical improvement in HTTPs protocol communication with NCBI
• Graphical Sequence View: improved rendering for translation discrepancies
• Graphical Sequence View: improved handling of tracks, added new data
• Text View: improved robustness when showing data from incomplete projects, when some links to local data cannot be loaded

Bug Fixes and Improvements

• Graphical Sequence View: fixed crash when two views are open and use track range broadcasting
• Graphical Sequence View: improved protein alignment rendering to pick more precise translation table
• Graphical Sequence View: improved tooltips formatting and positioning
• Text View: fixed issue on MacOS with disabled “Select All”

Release Notes for Genome Workbench 2.11.5 (November 14, 2016)

New Features

• Use of encrypted HTTPs protocol for back-end communication for VDB/SRA based annotations
• Multiple Alignment View: reworked to use feature renderings from Graphical Sequence View
• Multiple Alignment View: added consensus option to BLOSUM coloring methods
• Open File: implemented loading multiple feature tables at once (used to be only first file)
• Open File: implemented reading of ‘Text Alignment’ format (FASTA Alignment) used by third party tools like MUSCLE
• Graphical Sequence View: Six-frame translation track – new option "Left-to-right translations" now correctly works if we flip orientation
• New tutorial for Coloring methods in Multiple Alignment View
• Readers: improved FASTA reader messages, modified GFF3 reader to keep GFF3 alignments as single alignments

Bug Fixes and Improvements

• Text View: fixed bug of not opening certain files
• Search View: fixed crash trying to run tools directly on searched objects without adding to the project
• Tools Dialog: fixed issue with incorrect molecules shown due to errors in selection processing
• Graphical Sequence View: fixed issue showing some extra amino acid in ProSplign alignment in intron part
• Graphical Sequence View: fixed rendering of protein/DNA alignments across splice junction
• Graphical Sequence View: fixed alignment drawing (bug was to extend it one position farther sometimes)
• Graphical Sequence View: corrected tooltip wordings for ORF
• Graphical Sequence View: fixed expansion of features in dbvar track
• Alignment Span View: fixed issue with incorrect Exon/Intron boundaries for amino acids encoded across a splice junction shown
• Sequence Text View: fixed appearance issue on MacOS (text overlap with Find label)
• Tree Viewer: search query performance optimized
• Open Dialog: fixed issues with posting BLAST RID from NCBI web site (it was shown as hyperlink, not text)
• Generic Table View: export improved to quote text fields to be more compatible with data, which includes commas and improve import into Microsoft Access
• Readers: handling the precursor_RNA feature bug fixed in GFF3

Release Notes for Genome Workbench 2.11.0 (October 6, 2016)

New Features

• Use of encrypted HTTPs protocol for back-end communication
• Improved ProSplign tool
• Improved support of Genomic Assemblies, so it is possible to run a tool (like BLAST) against sequences in it
• New documentation: Soft clipped sequences, Using Tree View, Selecting visible columns
• Graphical Sequence View: added display option to show soft-clipped sequences in alignments

Bug Fixes and Improvements

• BLAST Search: fixed incorrect processing of queries based on selected range
• Improved stability in situations when it works standalone, without any network
• Text View: fixed Select All on MacOS
• NG Aligner Tool: added sort options to for Query and Subject sequences
• Graphical Sequence View: fixed event handling freeze for two coordinated views
• Graphical Sequence View: improved tooltips to avoid duplicate information, better formatting of mate pairs
• Graphical Sequence View: graph track rendering improved to better reflect areas with no values
• Graphical Sequence View: improved rendering of features to avoid overlap with strand indicator
• Tree View: fixed broken tree label editing
• Tree View: improved performance of bounding box tree markup
• Tree View: add “do not sort” option to Sort menu
• Dot Matrix View: improved to better combine alignments together to open in one view
• Export improved to better classify possible variants available with or without data type conversion
• Improved BED format import: added support for feature coloring instructions
• BAM support: improved graph generation time, added various optimizations

Release Notes for Genome Workbench 2.10.7 (June 24, 2016)

New Features

• BLAST Tool: added support for local custom BLAST databases
• Graphical Sequence View: added log scaling option for graph tracks
• Generic Table View: new tutorial added

Bug Fixes and Improvements

• Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
• Tree View: layout updated to better accommodate nodes of different sizes
• Table Import Dialog (MacOS): fixed issue with table visibility
• Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
• Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
• Graphical Sequence View: fixed protein coloration methods
• Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
• Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
• Search View: ORF Finder – fixed incorrect protein lengths
• Fixed bug with not opening project file (.gbp) on a click
• Fixed issues in GVF import
• Fixed BLAST Search tool against NCBI databases not working
• Fixed tblastn (protein BLAST) not working in standalone mode
• Fixed GTF export failure

Release Notes for Genome Workbench 2.10.5 (April 25, 2016)

New Features

• New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
• New export function for BAM/cSRA coverage graphs (Tutorial)
• New export function for alignments GFF3 format ((Tutorial))
• Tree View: implemented new export mode based on selections (tutorial coming)
• Tree View: added support for distance based circular trees
• Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
• Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

Bug Fixes and Improvements

• Alignment Table Export: fixed selection of correct alignment objects for export
• Text View: fixed incorrect display for SNP/variation feature after a feature search
• Sequence Text View: fixed crash on text search
• Open File Dialog: fixed MacOS crash in File Import if user attempted to delete existing open items
• Graphical Sequence View: fixed issues with alignments coloration for protein to nucleotide alignments
• Graphical Sequence View: tooltips for SNPs freeze fixed for MacOS
• Graphical Sequence View: improved retrieval of segment map for sequence
• Graphical Sequence View: new feature 'Project features from aligned sequences' allows to see protein when zooming in to sequence level on CDSs
• MacOS: fixed random crash on exit
• Search View: fixed crash when adding a gene to a project
• Run Tool Dialog: fixed object selection issues
• Run Tool Dialog: improved to offer a full parent molecule (not just a selected range), similar to Active Object Inspector
• Run Tool Dialog BLAST: improved to remember column widths in tables
• Windows: fixed issues with not being able to use more than 2GB of memory on 64-bit OS
• Improved taxon label retrieval to be non-blocking
• Phylogenetic Tree Builder: improved to use accessions of molecules, not GIs
• New mechanism for new version update notification
• Alignment Span View: fixed export to CSV

Release Notes for Genome Workbench 2.10.0 (January 19, 2016)

New Features

• BLAST tool reworked to support search in local BLAST databases
• Tree View: new functionality to collapse multiple nodes based on selection or a query

Bug Fixes and Improvements

• MacOS-X: fixed crash related fonts and mouse event processing
• Generic Table View: fixed issues with opening sequences when viewing assemblies
• Generic Table View: CSV export now allows to select export columns
• Performance improvements loading WGS (Whole Genome Sequencing) molecules
• Improved compatibility with GFF format (format reader)
• Multiple Alignment View: fixed crash in setting Master sequence
• Multiple Alignment View: fixed issues with showing previously hidden rows
• Multiple Alignment View: fixed terminology for amino acids for protein alignments
• Graphical Sequence View: improved track names to better synchronize with the annotation labels coming from the data loaders
• Graphical Sequence View: fixed labels side overlap on some narrow views, fixed feature overlap
• Graphical Sequence View: improved alignments renderings to make gaps visible on small scale zoom level
• Graphical Sequence View: fixed issue with marker failed to disappear (just moves to position 1)
• Tree View: improved newick format compatibility
• BAM format support: improved index file name recognition
• FASTA import: fixed regression with processing ids of local molecules
• Search View: improved to better provide organism names
• Search View: fixed crash on opening search results
• Search View: fixed incorrect label for SNPs
• Alignment Span View: fixed issue with mixed alignments
• Text View: fixed cursor wait state
• Linux: Fixed visual glitch in PDF export dialog
• Project Save Dialog: fixed defaults for multi-project save (workspace)

Release Notes for Genome Workbench 2.9.5 (August 26, 2015)

New Features

• MacOS-X: added support for the MacOS 10.10 (Yosemite)
• Graphical Sequence View: added ruler for protein coding regions
• Dot Matrix View, Multi-pane Cross Alignment View: added Save to PDF export feature

Bug Fixes and Improvements

• MacOS-X: added support for the latest MacOS versions
• BAM file format support: fixed crash, improved exception and error handling when opening incorrect BAM files
• BAM format support: fixed crashes on loading certain accessions
• Alignments display: fixed issues with alignments referring to certain
• Fixed crash on startup in situations when network access to update service is unavailable
• Fixed remote access to certain type of accessions and annotations (VDB storage type)
• Graphical Sequence View: fixed “loading…” text in generated PDF
• Graphical Sequence View / Alignment Views: implemented a new color scheme for ATGC colors, it is now coordinated with SNPs. New color scheme is more friendly to certain types of color blindness
• Graphical Sequence View: improved performance of alignment rendering, scrolling of views
• Graphical Sequence View: fixed bug in export of alignments
• Tree View: fixed bug with node highlighting, when user cycles through the search results
• Tree View: improved performance of tree sorting when many views are open
• Tree View: improved tree-to-tree comparison (broadcasting selections)
• Search View: search of Genome assemblies improved to get more consistent results, which can be added to the Project.
• Broadcasting Options Dialog: fixed issues with saving options
• Project Tree View: improved performance of large projects (selections, actions on selected items, search, etc)

Release Notes for Genome Workbench 2.9.0 (May 05, 2015)

New Features

• Tree View: implemented custom selections and coloring for queries and clusters
• Graphical Sequence View: combined VDJ-segments and C-region features into the gene model track
• Graphical Sequence View: graph track improved to show negative numbers
• Tree View and Generic Table View: added support for wildcard search and phonetic search
• Tree View and Generic Table View: implemented broadcasting between Tree and Table if both views are open on the same data
• Project Tree View: new function to hide the disabled content

Bug Fixes and Improvements

• Fixed visualization glitch on showing certain BAM files
• Graphical Sequence View: improved renderings of recognition sites
• Graphical Sequence View: fixed SNP gray-scale rendering
• Open Dialog: Improved performance
• Open Dialog: improved saving locations (accessions with range)
• GFF load: improved column parsing algorithm, added more meaningful project items
• WIG load: improve spec correctness
• Tree View: fixed issues with not remembering custom label settings
• Tree View: fixed issues with visual area jumping to a new location after search, even when search target is already visible
• Fixed crash on empty tree file
• Active Objects Inspector: fixed bug on not showing selection size
• Active Objects Inspector: improved performance in Brief and Full mode
• SPLIGN Tool: added function to add accession manually
• BLAST Tool: improvements and fixes to eliminate crash on run
• Implemented "Reset" button for SPLIGN, Find Overlap, BLAST Search and BLAST Sequences
• Tools/Options: added new option to change or disable the auto save interval

Release Notes for Genome Workbench 2.8.10 additional build (February 05, 2015)

Bug Fixes and Improvements

• Fixed crash on MAC OS X 10.10 (Yosemite)

Release Notes for Genome Workbench 2.8.10 (January 16, 2015)

New Features

• Added support for Ubuntu 14.04
• Implemented automatic project save and restore on restart (if software crashes)
• Implemented saving of windows positions (docked and floating)

Bug Fixes and Improvements

• Fixed crash on Ubuntu 14.04 when selecting a range in graphical sequence view
• Fixed crash when vertically stacking views
• Fixed issue with windows move, not redrawing correctly
• Linux and MacOS – fixed issues with on-exit hanging
• Tree View: fixed crash with stack overflow of large trees
• Tree View: fixed issue with queries, going into loop (with blinking screen visual effects)
• Tree View: fixed broadcasting between same tree open in different views
• Tree View: improved settings save and restore after restart
• Tree View: improved PDF output to consider left/right top/bottom margins
• Tree View: Settings dialog layout fixed not to clip dialog controls (transparency factor)
• Graphical Sequence View: fixed crash on moving tracks in Multi-level mode
• Graphical Sequence View: fixed display issues with Clinical variants track
• Graphical Sequence View: improved feature (depth) discovery algorithm
• Graphical Sequence View: improved PDF renderings of markers, fixed issue with unnamed markers
• Graphical Sequence View: improved rendering of links in tooltips
• Graphical Sequence View: fixed bugs with disabled alignments sometimes remained visible as a track
• Sequence Text View: fixed crashes in rendering and color changing
• Text View: fixed hanging issues when searching
• Text View: fixed crash on some keyboard + mouse combinations
• Text View: fixed crash on Linux when user tries to paste something
• Text View: improved toolbar usability
• Multiple Alignment View: fixed issue with columns visually overlapping
• Newick tree format import – fixed format detection algorithm (was misdirecting as BED format)
• Open View Dialog: fixed issues with being unresponsive after data conversion
• Open View Dialog: fixed search/filtering functionality

Release Notes for Genome Workbench 2.8.0 (August 18, 2014)

New Features

• Implemented export of Alignments (BAM, cSRA) to tab delimited format (MS Excel) (see Working with BAM files Tutorial)
• Implemented new flexible broadcasting between bio trees, based on prioritized list of node properties (see Broadcasting Tutorial)

Bug Fixes and Improvements

• Genome Workbench upgraded to use new version of wxWidgets 3.0.1, fixed some MacOS issues
• Search View: fixed issue with loss of Strong Kozak signals
• BED reader: fixed crash on certain files
• GFF reader: fixed some compatibility issues
• Cross Alignment View: fixed crash
• Fixed crash on Linux and Mac on minimization of some views
• File related dialog – added extra checks for file/path validity
• BLAST Search Tool: performance optimization of dialogs opening, better handling of long tasks
• Open Dialog – Genomes: fixed bug with showing duplicate items
• Run Tools dialogs: performance optimization
• Text View: ‘Find’ improved hot-key processing (Ctrl+A to select all)
• Open Dialog: MacOS fixed access to recently used projects and workspaces

Release Notes for Genome Workbench 2.7.19 (June 03, 2014)

New Features

• Text View – improved searching, added case sensitivity search option
• Open Dialog – added history list for opening GenBank molecules by accession

Bug Fixes and Improvements

• Graphical Sequence View: fixed crash on competing multi-threaded redraw
• Fixed network connection issues on certain networks not reporting correct DNS address
• Improved GFF3 import
• Fixed BAM/cSRA files opening when BAM file is located on Windows local or network mapped drives
• Sequence Text View - fixed crash on color change
• Fixed crash with dragging Project Tree Window
• BED file import – improved remapping using information from genomic assemblies
• Tree View – improved broadcasting mechanism with Tree View and Generic Table View
• Tree View – improved wait cursor for certain operations that may take a long time
• Tree View – fixed bug with viewport and scrollbars render incorrectly after maximizing or un-maximizing a window
• Tree View – fixed bug in Search function (it required two clicks to start)
• Tree View – PDF export, fixed bug with missing labels when working using Remote Desktop
• Active Objects Inspector – improved display of selected rows from Generic Table View
• Dot Matrix View – fixed crash
• Open View Dialog – fixed issue with unnecessary extra rows when selecting regions for display
• Multiple Alignment View – fixed OpenGL issue on Intel integrated graphics card
• Generic Table View – improved search function to better search for phrases
• Text View – fixed issues with non-displaying ASN.1 types when switching to and from the ASN mode
• About dialog – design change, use hyperlink to open the website

Release Notes for Genome Workbench 2.7.15 (February 14, 2014)

New Features

• Multiple Alignment View: implemented adaptive feature display when zooming in
• Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
• Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements

• Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
• Multiple Pane View: fixed crash on loading BLAST results
• Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
• Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
• Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
• Text View / Flat File: fixed Mac OS rendering issues
• Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
• File Import: optimization improvement to speed up load of files containing multiple project items
• File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
• Mac OS: improved tooltips for toolbar buttons
• Phylogenetic Tree Builder Tool: improved diagnostics of errors
• Multiple Alignment View: optimizations to avoid main GUI freezes
• Open Dialog: removed duplicate elements in table of genomes (load Genome)
• PDF export: fixed issue with XREF table errors
• Tree View: fixed issues with showing Force Layout progress on Mac OS
• Tree View: PDF export fixed issues for showing labels of collapsed nodes
• Tree View: added an option to stop layout
• Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Release Notes for Genome Workbench 2.7.12 (December 16, 2013)

New Features

• New improved GFF format reader
• New Tree Renderer with improved speed
• Data import redesigned to support molecule id mappings from local to NCBI accessions using genome assemblies
• Open View dialog now implements filtering/search, making it easier to find the right object (for example alignment)
• Graphical Sequence View: implemented visualization for map data records representing restriction maps or other non-sequence based maps such as MAP_000012.1. For more details see Graphical View legend

Bug Fixes and Improvements

• Fixed crash on unloading/renaming/moving of project items
• MacOS: fixed failure to run BLAST in standalone mode
• Improved BED import
• Tree View: improved custom label to be set separately for each tree (it was a global setting before)
• Tree View: fixed crash in Force Layout display mode
• Tree View: improved label pattern parsing to avoid incorrect labels
• Improved OpenGL rendering compatibility with regard to various drivers
• Fixed OpenGL bug with access to rendering prior to context creation
• Multiple Alignment View: fixed crash with alignment coloration (Column Quality Score)
• Multiple Alignment View: fixed issue with graphics scale factor with column resize
• Multiple Alignment View: improved tooltip content, implemented new sticky tooltips
• Multi Pane Cross Alignment View: fixed crashes and failures to open
• Improved GTF export dialog and code
• Sequence Text View: fixed crash by better handling of internal exceptions
• Improved system response on bulk deletion of project element (a potential crash fixed)
• Fixed issues with generation of project item labels for imported data
• Graphical Sequence View: fixed bug with displaying scaffold and component maps
• Graphical Sequence View: fixed incorrect tooltip pointer for flipped strand display mode
• Graphical Sequence View: PDF export, fixed bug with missing empty tracks in the final
• Graphical Sequence View: Fxed bug with opening wrong alignment despite the cursor selection
• Graphical Sequence View: tooltip improvement to show “comment”
• MacOS: fixed some cases of program freezing on pasting data
• Improved compilation for OpenSUSE
• Windows/OpenGL: fixed critical problem with incorrect zoom after showing dialogs
• Generic Table View: improved to show sequence ids as a column
• Improved error message diagnostics for tools
• Find Overlap tool: improved stability, logging and canceling
• PDF export: fixed interaction issues with PDF Save dialog
• Improved file format detection for compressed (gzip) files (file import)
• Linux: fixed Drag and Drop for Open Dialog

Release Notes for Genome Workbench 2.7.6 (June 3, 2013)

New Features

No new features were added during this release.

Bug Fixes and Improvements

• Graphical Sequence View: Fixed issues with missing feature track “Others”/”Misc”
• Graphical Sequence View: Fixed issues with displaying unaligned tails
• Graphical Sequence View: PDF export fixed coordinated bug when setting range, fixed issues on Linux
• Graphical Sequence View: six frame translation track – fixed translation table for mitochondrial sequences
• Graphical Sequence View: Improved alignment statistics in the tooltips now showing both base count and base percentage
• Find Overlap Overlap Between DNA Sequences tool: fixed instability, correctly implemented tool cancel function
• Fixed crash on cleaning internal cache database
• Table Import: improved handling of invalid values
• Create Gene Model tool: improved error handling
• Tree View: Fixed rendering issues on with some Linux drivers, force linux to use standard source alpha blending as we also do for OpenGL 1.1
• Tree View: fixed transparency factor settings dialog
• Multiple Alignment View: fixed tooltip window size to better fit text on Linux

Release Notes for Genome Workbench 2.7.5 (May 13, 2013)

New Features

• Sequence View and Tree View now support publication quality image export (PDF). Graphics can now be used for presentation printing in high resolution. (Publication Quality Graphics (PDF Image Export) Tutorial)
• Graphical Sequence View: new context menu function Load Default Tracks to restore track configuration
• New Projects and Workspaces Tutorial
• New reader to open text alignment files

Bug Fixes and Improvements

• Graphical Sequence View: improved marker details dialog
• Search View (MacOS): improved tooltips to correctly display full data description
• Search View (Linux): fixed autocomplete selection
• Linux: fixed application freeze related to status bar update
• FASTA Load: fixed critical bug which prevented multi-entry FASTA files to be loaded
• Generic Table View: fixed crash working with empty table
• Graphical Sequence View: fixed alignment score coloration issues
• Graphical Sequence View: fixed pseudo feature rendering
• Graphical Sequence View: fixed/improved tooltips (extra line break, SNP tooltips content, etc)
• Graphical Sequence View: fixed failure to group RNA and CDREGION features if gene is absent
• Graphical Sequence View: fixed tooltips generation of alignments with references on unresolved local sequences
• Graphical Sequence View: added support of whitespace as sequence position
• Multiple Alignment View: fixed tooltip
• Fixed bug in visible range broadcasting
• Fixed thread race crash related to caching taxonomic labels
• Table Reader: improved recognition of column delimiters
• Open View Dialog (MacOS): fixed “Command+A” key combination to select all objects
• BAM/cSRA compatibility: improved diagnostic messages for cases when sorting/indexing cannot work because of permissions and other restrictions
• ASN.1 files import: added support for direct opening of gzipped files (without need to decompress)
• NG Aligner tool: number of fixes and improvements
• Generic Table View/SNP View: fixed sorting of numeric (RSID) fields

Other notes

• Ubintu 10.04 and Genome Workbench builds for it are no longer supported

Release Notes for Genome Workbench 2.7.0 (March 18, 2013)

New Features

• New, reimplemented SNP Table View (SNP Table View Tutorial)
• Graphical Sequence View: implemented new persistent markers on sequences (Sequence View Markers Tutorial)
• Implemented reader of 5-column feature table format
• Text View: Implemented search
• Genome Workbench project can now be opened as Table (Project Tree View, project context menu / Open Table View). New feature allows user to sort and search project content.

Bug Fixes and Improvements

• Multiple Alignment View: added new column “Organism name” (taxonomic name)
• Multiple Alignment View: fixed issues with BLAST results with multiple queries
• BLAST Search: improved Blast DB selection from the most recently used list
• BLAST: improved parameters selection interface not to allow mutually exclusive options
• Graphical Sequence View: fixed crash with protein alignments
• Graphical Sequence View: fixed crash with visualization of pile-up graph for alignments
• Graphical Sequence View: improved 'Project features for aligned sequences' mode for alignment tracks
• Graphical Sequence View: fixed display of alignments with local ids
• Graphical Sequence View: restored defline as part of sequence track label, sequence track tooltip improved to be pinnable
• Graphical Sequence View: implement 5’ end visual tagging (sequence track)
• Splign tool: fixed crash
• Table Import: improved recognition of DOS/Unix line breaks, various small issues fixed
• OpenGL support: resolved issues with some limited functionality graphics drivers, improved work with Remote Desktop
• Tree View: improvements and fixes for PDF printing
• Generic Table View: implemented support for Copy from cell function
• Generic Table View: added support for disabled rows
• Table Views (all): added pop-up tooltip to show full content of extra long cells
• VCF support: improved label generation for VCF imported variants
• Alignment Summary View: fixed number of bugs and issues
• Text View: implemented molecule separation in Flat File mode
• Create Gene Model Tool: added option to propagate ncRNA features
• Status Bar: added explicit warning, when relaxed molecule id comparison is used in broadcasting
• BAM support: fixed crash working with network paths and some incorrect path locations
• Open Dialog: number of small GUI cleanups and improvements, improvements of MacOS copy and paste
• Broadcast Options dialog: save settings for program restart

Release Notes for Genome Workbench 2.6.5 (November 14, 2012)

New Features

• Add Tools Quick Launch items to context menu
• Graphical Sequence View: implemented separation graphs into sub-tracks based on meta-information title

Bug Fixes and Improvements

• Updated VCF and GFF readers, fixed issues with checking sequence ids
• Connection issues resolved for users running international versions of Windows or MacOS
• BLAST tool dialog freeze for a long time loading list of available BLAST databases
• BLAST RID load: fixed to automatically import both alignments and local sequences
• MUSCLE tool integration: fixed alignment coordinate remapping(shift error)
• Graphical Sequence View: fixed display of tracks with alt-loci alignments
• Graphical Sequence View: fixed fixed alignment score coloration for SRA
• Graphical Sequence View: tooltips improved alignment statistics and positions
• Graphical Sequence View: fixed indels rendering in protein-to-genomic alignments
• Graphical Sequence View: fixed empty tooltip lines (sequence)
• Multiple Alignment View: fixed tooltips to be displayed only over sequence part
• Linux: improved README for users building custom Genome Workbench
• Search View: fixed failures handling multiple sequence ids
• Search View: Kozak patterns updated
• BAM/cSRA support: fixed Open File masking for MacOS and Linux
• Text View: fixed crash in Flat File mode
• Tree View: fixed view title after tree sort operation
• MacOS: fixed opening projects from network paths/mappings/mountpoints
• MacOS: fixed issues with pasting into Open View dialog
• HTTP connection component: fixed "User-Agent:" self-identification to better conform standards
• Improved logging and Feedback reporting not to collect potentially sensitive information

Release Notes for Genome Workbench 2.6.0 (August 31, 2012)

New Features

• Search View: Implemented SNP Search (search by NCBI rs id)
• File Open: implemented support of direct file open from compressed formats .gz and .bz2
• Generic Table View and Tree View now remember old queries and search terms
• Generic Table View: new context menu option to filter on this cell
• Tree View: implemented broadcasting of taxonomic ids (tax-id property) to facilitate interactive comparison of trees
• Multiple Alignment View: new tooltips with detailed statistics for row and column

Bug Fixes and Improvements

• Format auto-detection for opening multiple files improved. First file is used for format detection analysis.
• Graphical Sequence View: major improvement in speed of rendering of BAM/cSRA alignments
• Graphical Sequence View: when selecting a region by mouse show exact boundary coordinates to improve position accuracy
• Graphical Sequence View: "Go to Sequence Position/Range..." fixed bug with focus in the dialog
• Graphical Sequence View: various fixes and improvements displaying of alignments
• Search View: fixed crash on feature search (“Select Feature Types”)
• Search View: fixed crash on closing the view while search in progress
• SPLIGN Tool: exposed more parameters for the algorithm
• Improved Drag-n-Drop of files into Project Tree
• Graphical View and Alignment Span View discrepancy fixed (rows selection made visible in Selection View)
• MacOS-X: improved windows docking
• MacOS-X: Application specific data now put into more conventional location for Mac platform
• MacOS-X: fixed bug with scroll bar disappearance in Graphical Sequence Viewer
• ORF/Kozak finder: fixed crash related to multi-threading
• File Open Dialog: improved layout to fix some cosmetic issues
• Tree View: Fixed bug with OpenGL rendering of mini-map (“m” key)
• Tree View: fixed issues in scaling of bounding boxes (cladogram mode)
• Window Manager: fixed number of issues which could cause crashes and incorrect window layouts
• Genome Assemblies – Generic Table View: added new columns: 'Assembly unit' and 'Patch type'
• Genome Assemblies – Grahical Sequence View: added support and visualization of of alignments coming with assembly
• Run Tool Dialog: improved default selection of target project for result
• Text View: fixed crash
• Feedback tool: improved e-mail address validation
• BLAST Search Tool: new improved categorization of available BLAST databases
• NG Align tool: algorithm rework and code cleanup
• Added support of new types of molecule accessions
• Linux: fixed number of dialogs where radio buttons did not work
• File Open/Import: improved default naming of project items, added meaningful track title for Graphical Sequence View
• File Open/Import: filename validation improved to be more responsive when used for slow network drives or locations
• Generic Table View: format of accession columns changed to include version number
• Generic Table View: fixed bug in query language, causing string interpretation of certain numeric types (like distance between nodes)

Release Notes for Genome Workbench 2.5.5 (May 17, 2012)

New Features

• Graphical Sequence View: saves markers and visual ranges (positions) on the sequence in the project file, reopening project now restores the context, making it easier to navigate.
• Graphical Sequence View: New rendering for clone features
• RMO format: added support for RepeatMasker RMP files (Feature Table)
• VCF format: added as supported file format for Open Dialog
• Implemented multiple-column sort option for tables (Search results, etc)
• BAM/cSRA: added support for SRA accessions in the Open Dialog
• Tree View: Search now supports wildcard espressions ‘?’ and ‘*’

Bug Fixes and Improvements

• Fixed multiple issues in processing and displaying alignments, due to switch to the new Alignment Manager (C++ Toolkit)
• Open Dialog (Genomes): fixed crash opening certain genomes like 'Escherichia coli'
• Open Dialog (Genomes): improved discovery of certain genomes (GRCm38)
• MacOSX:  Fixed bug when you click on list icon Float/Minimize/Close options are disabled when docked
• MacOSX: Fixed bug with menu items not always available
• MacOSX, Windows: certain command shortcuts changed to better satisfy platform standards
• MacOSX: Solved stability issues related to OpenGL on dual GPU MacBook Pro machines
• MacOSX: solved drag-n-drop issues between Project Tree elements
• MacOSX: fixed a major issue in windows layout
• File Export: added default extensions for files of different formats
• Tree View: performance optimization for various versions of OpenGL
• Linux: Fixed compatibility issues, related to various versions of libpng and its APIs
• Project Load: load of large project can now be canceled using context menu
• Labels generation: fixed crash
• Labels generation: improved performance of taxon labels bulk retrieval
• FASTA import/export: fixed bug with exporting duplicate sequence ids (which prevented opening the exported file)
• Graphical Sequence View: Fixed bug in selection broadcasting for results of Component Search
• Graphical Sequence View: improved rendering of backgrounds for mRNA features
• Graphical Sequence View: fixed direction of transcription are drawn backwards in alignments
• Graphical Sequence View: more options for alignment height
• Graphical Sequence View: improved rendering of mixed strand alignments
• Graphical Sequence View: improved rendering of protein to genomic alignments
• Graphical Sequence View: fixed bug with ProSplign alignments don't project up from NT to NC
• Graphical Sequence View: fixed crash related to hotkeys and local menu
• Generic Table View: added export into a separated file, readable by MS Excel (use context menu)
• SPLIGN Tool: crash fixed
• Tree View: fixed rendering of area markup
• Tree View: fixed crash if node is deleted in one tree and user goes to another tree
• Tree View: improved broadcasting of certain local sequence ids
• Multiple Alignment View: fixed crash on certain BLAST alignments
• Search View: fixed issues with server-side compatibility sometimes showing empty columns
• ORF Search: crash fixed
• Genome Workbench now uses wxWidgets 2.9.3, fixing lots of issues on various platforms
• Close Workspace Dialog: layout fixed
• Alignment Summary Report: fixed to show 1-based coordinates (was: 0-based)
• BED Import: improved compatibility with BED format

Genome Workbench 2.5.0 Release Notes (1/11/12)

New Features

• Added support of Genomes (user can now search and load genome information (collection of sequences) from NCBI into project.
• BAM files loader now integrated with genome information from NCBI
• Added support for a new cSRA file format
• MacOS-X 64-bit build added to our distribution list

Bug Fixes

• GFF reader optimized for better performance, file size and memory footprint
• Improved communication protocol for clients working with certain versions of not so standard firewalls
• Graphical Sequence View: improved clone feature rendering
• Graphical Sequence View: fixed incorrect selection broadcasting
• Multiple Alignment View: fixed memory leak causing major slow down or crash on large data
• Text View: can now show ASN.1 type information
• Text View: fixed bug in range display for FASTA format
• Tree View: fixed crash on entering letters for cluster ids
• Tree View: improved performance and fixed some issues with radial layout
• Improved performance of generating a meaningful description for sequences
• Export of annotations in ASN.1 format: fixed issues of files written incorrectly, so binary ASN cannot import back to Genome Workbench
• Generic Table View: implemented cell de-selection, improved object broadcasting
• Generic Table View: accessions and locations made clickable
• Search View:  fixed bug with incorrect row selection when sorting
• Search View: fixed bug on searching for components
• New version notification dialog: improved UI to offer a clickable URL
• BAM file loader: fixed file permission issues on MacOS-X
• BAM file loader: allow to select more than one file at once
• Open Dialog: improved performance opening a project item with large number of objects (like Genome collection)
• Open File Dialog: fixed issue with sometimes incorrect file opening on Windows
• FASTA load: performance optimization
• Project Save and Load: improved progress reporting, so Genome Workbench does not look dead while it is just busy

Genome Workbench 2.4.5 Release Notes (10/18/11)

New Features

• Open Dialog now implements a default view functionality, user can now open default view with a mouse double click in the project tree
• Generic Table View: implemented search function and query language
• Generic Table View: implemented new option to open trees as tables
• Tree View: implemented distance (scale) bar for trees with distances (like phylotrees)
• Graphical Sequence View: improved tooltips, links to RefSeq Gene, Entrez WEB pages added
• GFF3: major version upgrade for GFF reader
• Text View: implemented data types display for ASN.1 mode

Bug Fixes and Improvements

• Multiple Alignment View: fixed memory consumption and crashing issues
• Graphical Sequence View: optimization of density graph computation
• Graphical Sequence View: fixed tooltips popup when dialog is shown
• Graphical Sequence View: fixed duplicate genes when project items annotate gene twice with an additional location
• Graphical Sequence View: fixed function of Undo-Redo buttons
• Graphical Sequence View: Fixed rendering issues of alignment statistics graphs at certain zoom levels
• BAM files compatibility:
• Tree View: improved search function
• Tree View: fixed crash when large tree is viewed with a change of layouts
• Tree View: fixed some sizing errors when certain trees become not fully visible after changes in zooming mode from vertical to proportional
• Tree View: fixed layout calculations and display of small single-node trees
• Tree View: fixed function of Undo-Redo buttons
• Tree View: fixed issues with nodes expand-collapse actions
• Tree View: fixed rendering issues with not always cleaning the view port area
• Local data caching: fixed bug in the internal SQL statements causing old data to stay in the database longer than expected
• Selection Inspector: fixed bug with scope selector disabled on MacOS
• Project Tree View: fixed crash when project item moved from one project to another
• Improvements and fixes of communication protocol to better work with older version semi-compliant proxy servers. This improvement results in better connection to NCBI data servers.
• Search View: MacOS version fixed autocomplete prevented entering new data
• Open View dialog: fixed location duplications
• FASTA export for BLAST alignments, fixed issues with showing incorrect locations in dialogs
• FASTA loading performance optimizations, use more advanced memory mapped I/O where possible
• Generic Table View: fixed graphical rendering issues (extra vertical lines) on MacOS
• Text View: now saves view settings (fonts, etc)
• MacOS: fixed various GUI issues related to keyboard commands and zooming using main menu, About not working, etc

Genome Workbench 2.4.0 Release Notes

New Features

• Tree View: implemented tree filtering using query language with logical expressions
• Implemented a brand new view: Alignment Summary to display various alignment properties (Identity %, Coverage %, mismatches, gaps, e-value, etc) in form of a tabular grid
• Implemented new column options for all table views to show/hide column, specify sorting and sort order
• Graphical Sequence View: ergonomics improvement, view now preserves collapse/expand state of track during Genome Workbench execution session
• Search Tool: overhaul of ORF Finder and Kozak Scan algorithms
• Graphical Sequence View: implemented context menu item Rename me to change track name
• Graphical Sequence View: user interaction improvements: '+' or '-' sign clickable on the left side of a track title bar, implemented track cloning
• Graphical Sequence View: 6-frame translation and protein translation are now context aware and can use alternative genetic code tables
• Graphical Sequence View: implemented alignment summary and statistics graph for alignment tracks (like BAM)
• Graphical Sequence View: implemented easy access to help and documentation

Fixes

• Fixed bug with incorrect taxonomic id when searching for a nucleotide in NCBI public databases
• Fixed Merge Alignment tool to use the same engine as Cleanup Alignment only with more exposed parameters
• Fixed bug with BLAST tool not honor multiple query sequences
• Fixed bug with tooltips sometimes stealing focus from views, so keyboard shortcuts may not work as a result
• Implemented new BLAST results retrieval from NCBI to improve stability over unfavorable network conditions
• Graphical Sequence View: fixed display of component map in multiple level layout
• Graphical Sequence Viewer: fixed bug in reading self-alignments, which caused alignments visualization duplication
• Graphical Sequence View: fixed rendering of multi-location fuzz rendering
• Graphical Sequence View: fixed alignment coloration mismatch
• Graphical Sequence View: fixed freezing opening more than one view at the same time
• Graphical Sequence View: fixed crash in six frame translation track when switching between multiple layout mode and default mode
• Fixed bug in reading alignment segments, which in some cases manifested as failure to open Multiple Alignment View
• MacOS-X: fixed bug with loading local caching plugin
• MacOS-X: fixed crash on drag-n-drop project items
• MacOS-X: fixed WindowMasker tar file download creates incorrect file permissions on Mac and Linux
• Selection View: fixed coordinate discrepancy bug
• Open View Dialog: fixed object grouping mode (feature tables failed to open)
• Open View Dialog: fixed "attempt to access NULL pointer" error
• Alignment Views: fixed view opening to better categorize alignments
• Fixed serious issues in layout and windows management
• Tree View: fixed crash on closing
• Search View: fixed thread races crash
• Search View: fixed issues with buttons Start and Stop became enabled simultaneously
• Search View: fixed component search coordinate error (it was giving +1)
• Search View: improved stability of ENTREZ search
• Search View: column width changes are now saved
• BAM reader: fixed bug opening files on network drives
• BAM reader: fixed issue with canceled opening tasks stays on in the Task View
• GTF/GFF import: incorporate better reader

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Genome Workbench 2.3.2 Release Notes

New Features

• Sequence Viewer: implemented fake end rendering for clone features
• ORF Search: implemented new column (Start Context), showing residues preceding and following ATG

Fixes

• BLAST and Windowmasker cannot start on Windows (missing manifest files)
• Sequence Viewer: fixed Marker navigation direction issue (Alt+left arrow)
• Tree View: performance optimization for large tree label assignment

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Genome Workbench 2.3.1 Release Notes

New Features

• BAM/SRA format support. Please see tutorial 6
• CLUSTAL execution added (as an external tool).
• Tree View: implemented image export to assemble panorama images and/or printing
• Tree View: implemented support for Zoom to Selection
• Implemented progress indicator when Genome Workbench accessing network services.
• Implemented progress indicator and cancel for View Open function (if it takes too long to convert objects)
• Graphical Sequence View: multiple rendering improvements to better visualize large clusters of features (icicles), improve rendering of component color maps
• Graphical Sequence View: Improved six frame translation track, better codon detection, and visualization parameters
• BLAST tool: new option to link related hits together (for better visualization).
• Options dialog: checkbox to quickly enable/disable use of PROXY (for roaming users)
• Linux binary build is now based on Ubuntu 10.04 LTS (Lucid Lynx)

Fixes

• Multiple Alignment Viewer: fixed crashes on opening certain alignments with version-less accessions, fixed tooltip crashes.
• Fixed crash with View opening (improperly sent notifications)
• Graphical Sequence View: fixed crash in tooltips at the end of a sequence
• Window Masker directory path now saved between Genome Workbench executions
• Selection View fixed crash related to internal event races
• Tree View: fixed rendering for trees with negative distances
• Export Alignments: crash fixed
• BLAST tool: fixed algorithmic crash related to incorrect location mapping
• Newick tree loader: improved standard conformance
• Tooltips: made multiple improvements to better conform to standards of target platform (Windows, Linux, MacOS)
• Windows manager: fixed issues in panel configuration, making impossible to resize things to invisibility (and loss of GUI control), fixed bugs on loading incorrect configurations
• On-disk cache: improved automatic recovery if database got corrupted.
• MacOS support: cosmetic fixes in the status bar
• MUSCLE tool: fixed execution failure if path includes spaces

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Genome Workbench 2.2.2 Release Notes

New features

• More advanced network traversal for clients behind restrictive firewalls
• Documented Graphical Sequence Viewer rendering styles (Sequence Viewer legends)
• Tree View: Implemented new markup styles (Adding a Phylogenetic Tree View)
• Search for Repetitive Sequences Tool: integrated with Window Masker stats files
• Improved support for opening files located in directories containing international symbols
• Improved progress messages to inform user if Genome Workbench needs to run a network transaction and may look frozen

Bug Fixes and Improvements

• BLAST tool execution: advanced parameters are better understood by in-core BLAST
• Feature Table View: improved functionality to show features on chromosomes (used recursive lookup for features if annotations are placed on components)
• Open Dialog: improved performance for clipboard pasting long list of accessions
• Dot Matrix Viewer: fixed bug with combining certain alignments into one view
• Dot Matrix Viewer: fixed cases when open dialog shows empty list
• Dot Matrix View: fixed bug with opening objects (in some cases view incorrectly complained "Please select at least one object")
• Graphical Sequence Viewer: fixed crash on mouse over certain alignments
• Fixed cache database corruption, when running multiple Genome Workbench instances
• Fixed incorrect handling of certain Trace Archive Ti accessions
• Tree Viewer: fixed minimap corruption
• MacOS-X: cosmetic improvements in look and feel
• Open Dialog fixed number of copy-paste issues when working with large accession lists and on Linux
• Tree Export: added default file extension to file selection dialog

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Genome Workbench 2.2.1 Release Notes

Genome Workbench version 2.2.1 was an internal NCBI only release.

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Genome Workbench 2.2.0 Release Notes

New features

• New tool: NCBI Genomic Aligner (also known as NG Aligner)
• Feature Table View reworked to support more input types (locations, annotations, sequence ids)
• BLAST tool (local): implemented integration with WindowMasker, user can download a WindowMasker statistics from NCBI FTP and use it as a filtering option in Genome Workbench
• Tree View: implemented sticky tooltips. Genome Workbench now implements dialog to automate masks download
• Graphical Sequence Viewer: implemented meta-information load to quickly discover NAs (named Annotations), improved performance, reduced memory footprint
• Graphical Sequence Viewer: new tooltip system with sticky tooltips (works as a bookmark)
• Graphical Sequence Viewer: improved alignment tooltips to reflect PolyA and Unaligned tails
• Multiple Alignment View: added a new column sorting option: non-sorted
• Open Dialog: implemented ability to open data from Genbank (Accession) with a selected region
• SPLIGN tool: added "Max Intron Size" option (user defined Maximum Genomic Extent limit)
• Text View: supports opening with a molecule range (selection in Graphical Sequence View) to show list of features in flat GenBank mode

Bug Fixes and Improvements

• Tree View: fixed broadcast selection to better support various alternative sequence ids (GIs, accessions)
• Tree View: fixes and improvements in GUI switch to black-and-white color scheme
• Tree View: fixed zooming inconsistencies
• Tree View: fixed bug with failing to create a sub-tree with one single node
• Tree View: MacOS X: removed hard-coded font size, fixed size issue in Properties dialog, fixed empty space above scrollbar, lack of background color in search bar, incorrect button sizes
• Graphical Sequence View: fixed bug to show features (genes) that contain seq-loc with multiple seq-ids
• Graphical Sequence View: fixed display for trans-splicing (exons are on mixed strands). Example: AE014297.2, gene name: mod(mdg4), transcript name: CG32491-RT
• Graphical Sequence View: fixed massive feature duplication when user loads a local feature into the same workbench project
• Multiple Alignment View: fixed compatibility issues with alignments produced by MUSCLE, fixed crashes
• Multiple Alignment View: optimization to quickly stop background data processing if view closes or user collapses a row
• Dot Matrix View: fixed issue with unnecessarily opening multiple views, better support for multiple alignments display in one view
• Dot Matrix View: fixed bug with opening (not opening) certain types of alignments (Sparse-segs for multiple sequence)
• Text View: fixed FASTA mode crash on certain incorrectly formulated data (non-existing local accessions) (Supercontigs from Broad)
• Text View: Fixed flat file display for single feature (was: "feature not found")
• Text View: memory footprint reduced up to 30%
• Gene Model Tool: removed "Copy other features from record" option (disabled)
• Gene Model Tool: fixed crash in the algorithm
• BLAST tool (local): fixed bug in running tBLASTn (protein to nucleotide) in standalone mode
• BLAST tool (local): tuned parameters of BLASTn to make it more like MegaBLAST (failed to find certain hits before)
• Remote BLAST load: fixed thread race crash when loading results from an NCBI BLAST farm
• Sequence Search tool: Fixed bug with unimplemented reverse complement search
• Sequence Search Tool: Fixed bug with search in selected range
• Fixed GUI long lock on view closing
• Tooltips: fixed multiple bugs related to cross platform tooltip implementation (Linux, MacOS-X)
• Open Dialog: fixed bug with incorrect accession list save between Genome Workbench sessions
• Feedback report: Improved internal diagnostics to better track time of certain events
• Improved performance of saving options and settings
• Window Manager: restore minimized view by a single mouse click (ergonomics improvement)
• MS Windows build: discontinued support for Visual Studio 2005, base build platform becomes VS 2008

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Genome Workbench 2.1.2 Release Notes

Special Thanks

We are especially indebted to the NCBI C++ Toolkit team, whose patience and help in establishing a capable network setup and in establishing a baseline for Windows 7 installation was invaluable. We are particularly indebted to Aaron Ucko for his help with FASTA parsing issues; Eugene Vasilchenko for general help with object manager issues and debugging memory consumption issues; Anton Lavrentiev and Sergey Satsky for help in improving network setup; Vladimir Ivanov for help with Windows 7 setup; and Denis Vakatov for general support and dealing with our compressed schedule.

New features

• Added special build for 64-bit Windows 7, enables more views to be opened simulteneously.
• Graphical Sequnece Viewer:
• new rendering styles for feature qulity characteristics
• new feature to center view around marker position (available through context menu)
• Tree View:
• added black and white color scheme
• added mouse dragging and panning for trees
• added font size customization
• Multiple Alignment View:
• anchor row interaction improved to allow selection/expansion

Bug Fixes and Improvements

• Added an option to run BLAST as standalone, out-of-process program, fixes a lot of Genome Workbench stability issues.
• Graphical Sequnece Viewer:
• fixed hang on selection of certain CDS fetures
• fixed crash in tooltip for exon feature
• Reduced memory consumption of highly repetitive alignments
• BLAST search:
• fixed passing Repeats argument to NCBI server
• fixed error reporting from BLAST farm to client
• Fixed various errors related to GFF import
• Improved network connectivity test for clients behind firewalls with closed high ports
• Search tool: fixed error when searching for incorrect or misspelled words
• FASTA import/export: improved compatibility with gene export FASTA files or files with non-standard symbols in defline
• Improved local data cache corruption detection, implemented automatic recovery
• Tree View:
• fixed bug in edge color customization
• fixed Undo/Redo
• fixed issues with minimap drag
• fixed issues with search

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Genome Workbench 2.1.1 Release Notes

New features

• Implemented network availability diagnostics, report issues if Genome Workbench cannot connect to NCBI servers
• Graphical Sequence Viewer: added new tracks (OMIM genes, CCDS genes, pseudogenes, ncRNAs and non-protein-coding genes)
• Graphical Sequence Viewer: implemented '..' as a delimiter for sequence ranges
• Graphical Sequence Viewer: multiple improvements in variation features coloring
• Graphical Sequence Viewer: improved labels layout (side labels) for alignments and component maps
• Graphical Sequence Viewer: major improvements in component map visualization and coloring
• Tree View: implemented mouse based scroll/pan, improved user interaction consistency between grapghical sequence view and tree view
• Tree View: implemented sub-tree extraction
• Tree View: new rendering mode to highlight collapsed sub-trees (Ctrl-L)
• Search: Added sequence location to results
• MUSCLE tool: added support for the newer version 3.8
• Installer: improved installation for users without admin priviledges

Bug Fixes and Improvements

• Fixed crashes related to threading and multi-tasking
• Graphical Sequence Viewer: bug fix in rendering conceptual translation relative to protein product
• Tree View: fixed tree attributes and labels inconsistency for (Phylogenetic Tree and Common Tax Tree)
• Tree View: fixed crash on Undo
• Fixed crash on shutdown if user closes application immediately after start
• Dot Matrix View: fixed issues with displaying self-alignments
• Dot Matrix View: fixed issues related to lost high score hits (floating point rounding errors)
• Text View: fixed crash when displaying certain features
• Text View: fixed bugs with not showing protein sequences in Flat File mode
• Fixed issues with tooltips over OpenGL graphics for Linux and MacOS X
• Multiple Alignment View: [+] button now works for the Master row
• WindowMasker tool: improved stability
• Selection Inspector: fixed crash on switching between modes
• Selection Inspector: fixed MacOS X compatibility issues (support for Apple key)
• Project Tree View: improved MacOS X compatibility for tree elements editing

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Genome Workbench 2.1.0 Release Notes

New features

• New Tree Viewer rendering with improved labels visibility, better support of clusters (coloring), function to load external attributes, node selection broadcasting (based on sequence id)
• Improved Tutorial
• Added integration with external MUSCLE tool
• Graphical Sequence View: feature quality visualization (rendering styles for .partial., .pseudo.,
• Graphical Sequence View: support for non-consensus splice sites
• Alignment Span View: support for
• Graphical Sequence View: mouse over alignment reports sequence base position in tooltip
• Graphical Sequence View: new rendering for parent-child feature relationships
• Graphical Sequence View: New content options for Gene Model Track to show/hide genes distribution histogram
• Linux build: added 64-bit Linux build (Ubuntu 8.4 Hardy), implemented DEB distribution file creation
• File Open Dialog: Implemented dead item removal from most recently used list
• Implemented Common Taxonomic Tree for sequences tool, with support of FASTA files as a legitimate data source for sequence ids
• Project Tree View: Folder open/closed state preserved in the project file
• File Open dialog: added list of recently open files
• Graphical Sequence View: added support for the new Clone feature subtype
• BLAST search tool: added RID (task id) for the details box, implemented copy-paste for easier WEB integration
• Alignment Span View: added support for unaligned head-tail, support Introl-Exon(In/Del) (splign alignments)

Bug Fixes and Improvements

• Fixed GUI logic in the Project Save dialog
• Graphical Sequence View: fixed Zoom handler behavior (.z. key processing)
• Improved Windows installer and plugin loading mechanism to be Windows Vista and Windows 2003 compatible
• Graphical Sequence View: Fixed serious performance degradation when zoomed to sequence level
• Graphical Sequence View: corrected positions for CDS translation and protein sequence
• Fixed disappearing scrollbar (windows manager)
• Fixed Project Item description editing / saving
• Fixed Needleman-Wunsch aligner
• Multiple Alignment View: fixed thick lines rendering issue
• Graphical Sequence View: fixed View redraw in multi-level mode after a project change
• Improved alignment labels for Spliced Alignments
• ASN export: improved file name validation
• Graphical Sequence View: Fixed Disc alignment rendering
• Project Tree View: Folder Delete/Cut/Paste/Drag-n-Drop function fixed
• Open File Dialog: fixed bug when Back button was showing empty or incorrect page
• Graphical Sequence View: fixed bug in alignment statistics (coverage) displayed in tooltips
• Fixed crash when editing label for unloaded project
• MacOS-X Color Picker Dialog: fixed dialog to correctly apply color changes
• MacOS-X: Implemented About box dialog
• Graphical Sequence View: fixed crash in flipped strand mode
• Search Edit Box: fixed upper-lower case history editing
• Tree View: fixed context menu radio button display to better reflect changes in the layout
• Multiple Alignment View: fixed unnecessary redraw happened on unrelated change in the project
• Feature Table View: fixed crash when the view is closed before loading content
• Text View: fixed crash in renderer
• Fixed GUI stalls generating labels for objects containing multiple alignments
• Fixed crash in Search Panel
• Fixed multiple issues related to internal thread/task processing
• Fixed selection inspector update/refresh related to multi-pane alignment viewer

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