Release notes for Geneious
Version 4.8 (29 October 2009)
New features added in Pro version only:
- Fast de novo assembly - Capable of assembling 100,000 454 reads or 500,000 Illumina Solexa reads without a reference sequence in a few minutes on a desktop machine.
- New dotplot - capable of dotplotting genome sized sequences with brand-new controls (utilizes EMBOSS)
- Better handling of next-gen sized data - greatly improved speed and memory efficiency when dealing with large next-gen data sets
- Primer extension support - add a restriction site or other extension to primers and Geneious takes this in to account when testing the primer and using it for other analysis
- Trim by primers - screen for primers from the local database
- Batch export - export several documents to separate files in one step (File > Export > Batch Export)
- Color sequences according to their annotations ("By Annotation" option under Colors in the Sequence View)
- More powerful primer design on alignments and support for designing primers on assemblies
- FastQ file format import
- CsFasta file format import
- Qual file format import
- Add and Remove enzymes from enzyme sets and combine enzyme sets
- Search for individual primers from your database that match a sequence
- Option to find residues in the translation of DNA (Edit > Find in Document)
- Quality measures for chromatograms added to sequence view statistics (Confidence and Expected Errors)
- Extinction coefficient for proteins added to sequence view statistics
- Read length and coverage statistics for sequencing data added to sequence view statistics
- Sort sequences by name and other attributes in sequence lists, alignments and assemblies (right click in Sequence View and under Properties options)
- The EMBOSS tools plugin is now included with Geneious as standard (adds many functions)
- All models in a 3D structure can now be shown simultaneously in the 3D structure view
- Folders can now be copied between server and local database by drag and drop
New features:
- Pan in Sequence View by holding Ctrl+Alt while dragging (Command+Alt on Mac OS)
- Greatly improved local database start up time for users with large numbers of documents (takes effect after first start up of 4.8)
- Geneious export no longer offers compressed/uncompressed format, Geneious format is always compressed with .geneious extension
- Sequence view statistics can now be copied to the clipboard
- Improved display of multi-interval annotations and primers in the sequence view
Bugs fixed:
- Change residue numbering now works on circular sequences
- Notes can now be stored in the Server database
Patch 4.8.5 (4 March 2010)
Bugs fixed:
- Updated BLAST code to reflect recent changes to NCBI's output format- fixes BLAST
- Speed up loading of large documents in dotplot
Patch 4.8.4 (10 February 2010)
New features:
- Annotation generators which act on chromatograms now work on alignments and lists containing chromatograms
- More memory efficient indexing of documents and better handling of low memory when indexing
- Improved behavior of dotplot on blast hit documents
Bugs fixed:
- Fixed crash that was preventing NCBI blastx from working
- Referenced sequences are now retained on assemblies of up to 10,000 sequences
- GenBank importer now works on files with nonstandard indentation of base numbers
- Fixed crash when concatenating chromatogram and non-chromatogram sequences
- Fixed crash when trimming while assembling with a blast hit
- Alignments with many referenced sequences are now saved more quickly
- Fix sequence search crash when query sequence name is not a valid folder name
- Fixed crashes caused by reverse direction annotations on protein sequences (when sequence searching, copying or extracting)
- Fixed an issue for some 32-bit linux users where Geneious wouldn't start
- Fixed crash in primer design when working with an alignment containing both chromatogram and non-chromatogram sequences
- Fixed crash caused by removing sequences from an assembly or sequence list which have been used for another assembly
- Primer design and testing now ignores regions of ?'s (eg. missing regions in genomes)
- Vector NTI importer no longer fails on files with a period in field values
Patch 4.8.3 (18 December 2009)
New features:
- Option to search on either forward or reverse strand in Search for Motifs
Bugs fixed:
- Extract PCR Product no longer adds one incorrect additional base
- Fixed Geneious giving out of memory errors when reaching about 80% of the memory it should be able to use in 64 bit versions
- Correct extension is now listed on reverse primers which are added via Test with Saved Primers
- Fixed crash when undoing in the sequence viewer
- Fixed hang on startup
- Fixed crash when saving changes to an alignment/contig
- Fixed hang when saving changes in an alignment/contig
- Fixed crash after deleting all sequences from a blast results folder
- Fixed crash when viewing chromatograms corrupted by a bug in earlier versions of Geneious. The corrupted chromatogram data is partially recovered in Geneious 4.8.3.
Patch 4.8.2 (30 November 2009)
Bugs fixed:
- Fixed a bug that caused Smart Agents to become normal agents after restarting Geneious
- Reduced memory usage for sensitivity based denovo assembly
Patch 4.8.1 (25 November 2009)
New features added in Pro version only:
- Reference sequence assembly option to randomly choose between best multiple matches
Bugs fixed:
- Memory leak when viewing sequence search results
- Out of memory error when saving changes to large contigs
- Correctly handle extracting annotations with multiple intervals in different directions.
- Query centric view no longer incorrectly splits annotations apart when hide gaps in reference sequences is on
- Removing bases when trimming on alignments no longer unaligns the sequences being trimmed.
- Fixed crash and/or incorrect results when building several alignments or trees simultaneously.
- Primer design on circular sequences now correctly finds primers for regions spanning the origin
- Fixed incorrect rendering of annotations spanning the origin of circular sequences when zoomed out
- Fixed crash when restriction sites are found spanning the origin of circular sequences
- Fixed crash when editing a contig immediately after reverse complementing the entire contig
- Find in sequence and find motif now find sequences spanning the origin of circular sequences
- Document fields such as description are now preserved in an alignment built from a sequence list
- Fixed bug printing a zoomed in sequence view where it would zoom out under some conditions
- And a few other minor bug fixes
Version 4.7 (29 June 2009)
New features added in Pro version only:
- Query centric multiple alignment BLAST view - Every BLAST search now has a view tab with the query centric alignment
- Fast reference assembly - Can now assemble 100,000 reads to a reference in less than a minute
- ContigExpress (.cep) import
- Primer database - Select primer sequences from anywhere in your databases for testing
- 454 import and handling - Import SFF files then view and assemble the sequences to a reference
- Custom keyboard shortcuts - Choose a shortcut key for just about any action in Geneious (Preferences > Keyboard)
- Show translation by coding annotations or just for the selected region
- Translate alignments/contigs relative to the start of alignment or the consensus sequence
- Set a reference sequence in an alignment/contig and highlight disagreemets etc versus the reference sequence (right-click > Set as reference sequence)
- Change the font and style for selected taxa in the tree view
- Color nucleotide triplets by their translation
- New tabular view of annotations on sequences
- New view showing graph of sequence lengths
- Extract PCR Product operation added
- Automatic scaling of chromatogram height
- Sequence view remembers zoom level for next disagreement and Editing state for assemblies
- Original chromatogram files can now be exported even after editing a chromatogram
- Can now trim the consensus to the reference sequence (if present)
- Find ORFs and structure prediction now works on alignments
- Improved coverage graph - stays after editing and can highlight low coverage regions
- Improved contig view - can vertically compact the contig view so that multiple reads can appear in the same row
- Consensus alignment has option to create an alignment of the consensus sequences only (useful for comparing assembly results)
- Option in BLAST to fully annotate the hit summaries - eg feature annotations, taxonomy and other properties
- Option to design a reverse primer only added
New features:
- MacClade color scheme added
- Can select multiple regions simultaneously in the sequence viewer (by ctrl-drag selecting successive regions)
- Improved sequence/alignment/contig viewer performance. Can view contigs with 100,000+ reads
- Improved performance handling large numbers of sequences - Imported sequences are grouped into a single list document and existing sequences can be grouped manually
- Check for Updates Now added to the Help menu and General Preferences
Bugs fixed:
- Fixed long delay before results appear when a large operation is completed
- Other columns such as description and organism can now be consistently used as labels in tree and sequence view
- Distance matrix now shows up more consistently in Text View on tree building results
Patch 4.7.6 (22 September 2009)
Bugs fixed:
- Added support for Mac OS X 10.6 (Snow Leopard)
- Printing: Fixed the positioning of the Middle line of text view of BLAST alignments
- Query Centric Alignment: Query is not annotated
- Primers: Determine characteristics and testing are using default minimum GC
Patch 4.7.5 (6 August 2009)
Bugs fixed:
- Vector NTI import now retains user defined fields for all sequence file types
- Importing a file containing a single sequence no longer asks whether to create a sequence list
- Save as image file fixed for the sequence view
- Fixed crash when deleting bases across the origin on circular sequences
- License is now correctly loaded from a file if the free trial is still active
- Fixed issue when copying large files to Microsoft SQL server database
- Fixed issue where extracting a region from a circular sequence wouldn't produce a sequence
- Fixed issue where the selection would move erratically on circular sequences
Patch 4.7.4 (22 July 2009)
Bugs fixed:
- Extract now offers to reverse complement if an annotation on the reverse strand is selected
- When importing sequences Geneious now asks whether to import as a sequence list or individual sequence documents
- Fixed incorrect downloading of genomic contigs from NCBI (due to not reverse-complementing when necessary)
- When extracting primers and pcr products Geneious now asks what to do when the primer doesn't match the sequence perfectly (eg. when there is degeneracy)
- Google Scholar links in pubmed articles now work more effectively
- Built-in tutorial and sample documents updated
- Fixed primer design on RNA sequences
Patch 4.7.3 (16 July 2009)
New features:
- Zoom to a region by holding Alt and dragging the mouse in the Sequence View
Bugs fixed:
- Fixed sequence view occasionally discarding changes when saving when editing multiple large documents simulaneously
- Fixed an occasional crash when clicking undo in the sequence/alignment viewer
- Fixed intermittent crash when assembling reads
- Fixed an occasional crash when deleting results from a sequence search
- Primers: Design with existing now works with heavy degeneracy in target sequence
- Primers: Performance of testing degenerate primers improved
Patch 4.7.2 (8 July 2009)
New features added in Pro version only:
- Can now test all primers in your database against a sequence
New features:
- Added the ability to rename, remove and reorder sequences in a sequence list
Bugs fixed:
- Fixed stuck tooltips when switching to another program on Mac OS
- Fixed a bug that could cause a crash when searching the local database with an empty field
- Fixed a hang that could occur in a server database
Version 4.6 (9 March 2009)
New features added in Pro version only:
- Gateway® Cloning support - Add attB sites, perform BP and LR reactions
- Vector NTI database importer - Import all supported data types from a Vector NTI database in one step
- Assemble by name - Use names to assemble many groups of sequencing reads in one step
- Sanger GFF Import and Export - Attach annotations from a GFF file to a sequence or export annotations from any sequence to GFF
- Ability to change font sizes in the Sequence View
- Overlay annotations on the bases in the Sequence View
- Import Rebase proto and withrefm fromats
- Binning of traces and assemblies according to quality indicators
- Ability to save save assembly results to a new folder with a permanent report document
- Ability to edit the consensus sequence in the Sequence View
New features:
- An option to flip the tree view horizontally
- Purine vs Pyrimidine color scheme
Gateway is a registered trademark of Invitrogen Corporation
Patch 4.6.5 (19 June 2009)
Bugs fixed:
- Fixed a bug that caused incorrect NCBI Gene documents to be downloaded in some cases
- Fixed a bug that could cause a crash when searching the local database with an empty field
Patch 4.6.4 (5 May 2009)
Bugs fixed:
- Fixed a bug that caused tutorials to be imported with a page missing
Patch 4.6.3 (4 May 2009)
Bugs fixed:
- Fixed a bug where only the first 1400 bp of sequences were imported from Vector NTI archive files
- Fixed bug that prevented the loading of documents with special characters in the server database
Patch 4.6.2 (20 April 2009)
Bugs fixed:
- Fixed hang when starting up Geneious after trial license expires
- Fixed bug where vector contamination at end of sequence was not detected during trimming
- Fixed local blast file setup on Linux
- Vector NTI importer now correctly imports dates and multi-line comments
- Fixed crash in "Add database" when using Geneious Basic
- Alignment concatenations now have correct names for sequences
- Fixed crash when previewing "Save to image" for very large images
- NCBI no longer warns about ambiguous bases once for each sequence in batch search
Patch 4.6.1 (31 March 2009)
Bugs fixed:
- Fixed issue where the Sequence Viewer would not display quality information on a sequence with no trace in a contig.
- Fixed the EndNote importer.
- Improved the performance of the GFF importer
- Fixed an issue where the BLAST plugin was not compatible with some custom WWWBlast servers.
- Improvements to sequence editing.
- Improved splash screen :D
Version 4.5 (27 November 2008)
New features added in Pro version only:
- Unified Sequence Search - New BLAST searching interface including batch searching and improved handling of results
- New 3D Structure Viewer - Includes ability to select parts of a structure and modifying their appearance individually
- Real-time Restriction Analysis and ORFs - Find restriction sites and ORFs are now part of the Sequence View allowing real-time updating of sites as options are changed
- Similarity Color Scheme - New color scheme which colors residues in an alignment according to similarity
- Support for Sassafras K2 license servers
- Print just the visible region from the Sequence or Alignment View
- Added support for designing sequencing primers
New features:
- Send Feedback / Report Bug - New item in the Help menu to easily send us your comments or report a bug
Bugs fixed:
- Fixed issue where File -> Save As would delete Notes from a document
- SCF import now handles a wider range of files
- Fixed problems with corruption of trees when sequences are renamed in the alignment
Patch 4.5.5 (10 March 2009)
Bugs fixed:
- Fixed wrong genomes being downloaded due to NCBI changing their format
- Made NCBI server location updatable
Patch 4.5.4 (22 January 2009)
Bugs fixed:
- Fixed crash when assembling contigs
- Fixed bug where importing large Geneious databases would run out of memory
- Fixed clustal alignments not storing references to original sequences
- Fixed crash when viewing sequences with a large font size
- Fixed changes made to imported Newick trees (e.g. coloring nodes) being lost after restarting Geneious
- Fixed changes made PopSet documents being lost after restarting Geneious
- Fixed very slow performance viewing some contigs
- Fixed crash and occasional incorrect dates when searching NCBI's SNP database.
Patch 4.5.3 (22 December 2008)
Bugs fixed:
- Fixed a bug that could cause the Text View to crash and corrupt the search index
- Identical foreground and background colors in the similarity color scheme no longer cause a crash
- Setup of COGS BLAST will no longer crash when the NCBI plugin is disabled
- Send Feedback / Report Bug now uses the standard HTTP port
Patch 4.5.2 (16 December 2008)
Bugs fixed:
- Restriction site annotation generator respects enzyme set document
- Fixed unresponsiveness while loading large sequence in sequence viewer
Patch 4.5.1 (12 December 2008)
Bugs fixed:
- Fixed memory leak when repeatedly viewing sequences in sequence viewer
- Many other small fixes
Version 4.0 (5 September 2008)
New features added in Pro version only:
- Cloning operation - Insert into vector provides one-step insertion into a plasmid
- Plasmid maps - restriction sites and annotations on circular sequences are now shown with the label pointing to the region
- Tree coloring - branches and labels can now be colored in the Tree View
- DeCypher - Added support for searching using TimeLogic's DeCypher accelerator hardware
New features:
- Annotation Viewing - Labels are positioned intelligently outside of region markers at low zoom
- Quality information is now imported from .ace files if available
- Chromatogram quality values are displayed in the Text View
- Save As... (Ctrl+Shift+S) added to File menu
- Protein structures now display all amino acid and DNA sequences
- New sample documents
- PopSet results now downloaded in sets
- Added more annotation types with improved coloring
- Annotations downloaded from GenBank are given more informative names
Bugs fixed:
- Further improvements made to chromatogram import to support a wider range of files
- Annotations are now displayed correctly on sequences from NCBI Gene (broken by changes at NCBI)
- Fixed situation where residues may be highlighted as agreements incorrectly
- Disulfide bond annotations from UniProt are now displayed correctly
- Geneious will no longer create dummy drives on Mac OS if a network drive is disconnected
- Advanced search for Pfam now works
- It is now possible to design primers to surround a single base as the target
Patch 4.0.4 (31 October 2008)
Bugs fixed:
- Changed NCBI SNP service to use new XML format
- Upgraded Pfam to revision 23
Patch 4.0.3 (16 October 2008)
New features:
- It is now possible to limit by Entrez query when doing a BLAST search
Bugs fixed:
- Fixed some issues with upgrading from previous versions
- Fixed a bug that caused a failure to load or import some chromatograms that were valid before Geneious 3.8
- Can now import chromatograms that contain any ':' or 'S' characters
- Fixed display problems caused by the latest Java update on Mac OS
- Reduced text size in Text View of Pubmed documents
- Corrected residue numbering for blastx results to be of the translation rather than the nucleotide query
Patch 4.0.2 (17 September 2008)
Bugs fixed:
- Made it possible to edit and manually add primer annotations again
Patch 4.0.1 (15 September 2008)
Bugs fixed:
- Add annotation in the Sequence View now remembers last type used
- Improved layout of labels in circular and linear Sequence View
- Improved Sequence View responsiveness
Version 3.8 (30 June 2008)
New features added in Pro version only:
- GenBank flat and XML exporters - For all nucleotide and protein sequences
- Text view on GenBank documents - For sequences under 10K in length, the full GenBank flat record is provided as the text view
- Vector screening - "Trim Ends" lets you trim for vector contamination
- Support for sticky ends - restriction digest produces documents with sticky ends, and concatenation takes these into account
- More sample restriction enzymes sets - Blunt, 3', 5' and common enzyme sets
- Restriction analysis improvements - Find enzymes not cutting a sequence, and restrict the search for restriction sites to those that do not cut within a certain region
- Extract annotations - inverse - You can extract all regions of a sequence not covered by an annotation
New features:
- Sample NEB plasmids - Annotated plasmids from the NEB website are included in the sample documents
- Concatenation into circular sequence - Concatenation can preserve the origin of a concatenated circular sequence fragment
- Selected document count - status bar in document table informs you how many documents are selected
- Go To Position in sequence - Jump to a particular index in a sequence, or select a particular range
- Improvements to annotation rendering - New 3D look and other improvements
- Performance improvements in the sequence/alignment viewer
Bugs fixed:
- Go to next disagreement no longer prompts to save
- Undo in the sequence/alignment editor no longer causes crashes
- Primer design correctly evaluates all possible mismatches
- Server database monitors external changes to documents being viewed
- Many other small fixes
Patch 3.8.5 (14 July 2008)
Bugs fixed:
- Fixed crash when encountering invalid NCBI files which have no division
Patch 3.8.4 (10 July 2008)
Bugs fixed:
- Fixed N's being imported as M's for ab1 trace files
Patch 3.8.2 (8 July 2008)
Bugs fixed:
- Fixed failure to import some chromatograms and fixed crash when trying to view some chromatograms imported using previous versions of Geneious
- Fixed crash when translating annotations in some circumstances.
Patch 3.8.1 (4 July 2008)
New features
- Windows 64 bit distribution to allow you exceed the 1.5 GB maximum memory limitation of 32 bit systems.
Bugs fixed:
- GenBank flat importer: No longer strips the last character from each keyword
- Tree Builder: Now produces unrooted (instead of rooted) consensus from unrooted samples
- Server database: Saving changes to documents in some cases no longer reverts to displaying the previous version of the document
- Sequence logo graph: Fixed crash when viewing alignments of proteins containing stop codons.
- Find duplicates: Fixed crash when finding duplicates on some documents
Version 3.7 (6 May 2008)
New features added in Pro version only:
- Protein Statistics - Real time update of isoelectric point and molecular weight in the statistic section of the Sequence View.
New features:
- Plugin Manager - Download and install plugins from within Geneious and stay up to date with the latest plugin releases.
Patch 3.7.1 (29 May 2008)
Public API issue resolved, no functional difference to 3.7.0
Version 3.6 (13 March 2008)
New features added in Pro version only:
- Vector NTI Import - Including molecule, oligo, enzyme and citation archives as well as sequences (.gb/.gp) and alignments (.apr).
- Edit tracking - annotations are automatically created which record what residues have been changed.
- Coverage graph for alignments and contigs
- Convert sequences between RNA and DNA - Under the Sequence menu
- Strip alignment columns - An operation in the Tools menu to remove all columns containing only agreements/transitions/gaps from an alignment
- Sequence View: can now highlight agreements with the consensus. Can also highlight transitions and transversions from the consensus.
- Sequence View: Can now jump to next agreement/disagreement/transition/transversion.
- Sequence View: Fill from left - Hold down the alt key when deleting regions (or individual bases) to move bases to the left (instead of those on the right) into the deleted region
- Sequence View: Can now choose colours for annotation types (click on colour box)
- Universal Mac OS binaries added for Primers and MUSCLE - improved performance on Intel Macs
New features:
- Improved tutorial with links to extra information
- Main menu structure improved
- Dotplot shows dotplot of one sequence with reverse complement of another
- Clustal color scheme added to sequence view
- Documents can now be sorted by their read/unread status
Patch 3.6.2 (28 March 2008)
Features added:
- Added support for Clustal 2.0
Bugs fixed:
- Fixed a couple of residue numbering bugs in PDB documents
- Annotations are no longer turned on every time a document is edited
- A small number of users who upgraded were not able to start the new version of Geneious
Patch 3.6.1 (19 March 2008)
Bugs fixed:
- Annotations from NCBI Gene are now added correcly
- Ambiguous base codes are now translated correctly
- Muscle executable fixed for PPC Macs
- Assembly can now handle assembling U (uracil) to T (thymine)
Version 3.5 (25 October 2007)
New features added in Pro version only:
- Motif finding - Select Edit -> Find in Document... and use Annotate All
- Muscle Alignment - Available in the Alignment options window.
Based on the state of the art alignment program Muscle.
- Server databases - Store documents in a central and secure relational database, mutliple users
can work on the same data simultaneously.
- Linnaeus Blast - Evolutionary view of BLAST results. Select Tools -> Linnaeus BLAST...
- Degenerate primer design - Select an alignment and select Tools -> Primers -> Design Primers...
- Extract annotations - Searches a sequence for annotations matching your criteria and extracts them.
Select Sequence -> Extract Annotations...
- Consensus alignment - Align several alignments using the consensus sequence. Available in the
Alignment options window
- Improved trace trimming - Trimmed ends are kept for adjustment after assembly.
New features:
- Sequence view improvements - Graphs now stay in view always and the names are resizable.
- Preferences now stored in user's data directory - Preferences will not be lost when accessing data on a network drive from different computers.
- Added support for amino acids U and O (Selenocysteine and Pyrrolysine)
- Improved dot plot - Added a crosshair
Patch 3.5.6 (19 December 2007)
Bugs fixed:
- Fixed corruption of chromatogram data due to editing.
- Editing of note types now behaves correctly
- Can now create Pfam sequences from UniProt sequences
- Default memory setting for MUSCLE alignment is now correct
Patch 3.5.5 (30 November 2007)
Features added:
- Geneious now runs on Solaris 10! Some plugins using native code only work on x86 systems.
Patch 3.5.4 (22 November 2007)
Bugs fixed:
- NCBI blast: tblastx hit annotation is now in the right direction!
- Ignore gaps is now disabled when using highest quality consensus
- The alignment dialog ran off the screen with too many alignment methods
- Endnote files were not importing correctly
- Various bugs in the server database plugin relating to referenced documents
- The server database plugin now automatically sets up schema in database
- The Genbank importer now supports files from GeneSNPs database
Patch 3.5.3 (15 November 2007)
Bugs fixed:
- Improved support for customers whose license no longer allows free Pro upgrades
- Can now edit phylogeny documents
- Fixed crash when phylogeny document referenced alignment document that had sequences removed.
- Fixed hang when saving to PDF
- Fixed various bugs relating to the server database plugin
- Fixed some memory leaks
Patch 3.5.2 (1 November 2007)
Bugs fixed:
- Various crashes in the server database plugin
- Find in annotations on a sequence crash
Patch 3.5.1 (29 October 2007)
Bugs fixed:
- Temporarily hid server databases from agents and collaboration for
stability
- Memory leaks in some viewers
- Crashes in some viewers
Version 3.0 (13 April 2007)
Features added in Pro version:
- Contig assembly!
- Circular sequence viewer!
- Restriction Site Identification!
- Improved primer design including mismatching and testing multiple primers!
- Enhancements to the Sequence Viewer including viewing of translation and complement alongside sequences
- Sequence logo graphs
- Improvements to the Tree Viewer including collapsible subtrees
- Nucleotide alignment via translation and back
- New file importers: PIR, EMBL, GCG and Phylip
- PFAM database
- Remove duplicates function on downloaded documents
- Extensions to options available in structure viewer
- Local folders can now be moved (File -> Move Folder... or drag and drop)
- Highest quality base consensus
- Geneious users can chat with users of other Jabber clients, e.g. Google Talk
- Plus lots of minor features and improvements
Patch 3.0.6 (16 July 2007)
Features added:
- Better management of multiple concurrent user licenses
Patch 3.0.5 (04 July 2007)
Features added:
- Support for multiple concurrent user licenses
- Support for licenses with arbitrary periods
- Support for licensing all users on a computer
Bugs fixed:
- A workaround for a bug in Apple's tree implementation
- Changed an invalid reference in the tutorial
- Made the E-value column leftmost by default
- Provide option to not print circles on nodes in tree view
- Various bug fixes
Patch 3.0.4 (15 May 2007)
Bugs fixed:
- Crash installing plugins
- Profile alignment crash
- Contig assembly crash
- Problem translating sequences with single residue annotations
- Other bug fixes
Patch 3.0.3 (27 April 2007)
Bugs fixed:
- Crash when editing chromatogram alignments
- Crash when viewing chromatograms without quality information
Patch 3.0.2 (24 April 2007)
Bugs fixed:
- Crash disconnecting after chat
- Chromatogram document crash
- Crash when viewing trees renamed in 2.5
- Other bug fixes
Patch 3.0.1 (18 April 2007)
Bugs fixed:
- Crash deleting two sequences from an alignment
- Cannot download PFAM database files when there is an active smart folder
- Atom filtering broken in 3D Structure Viewer
- Saving notes on a large number of documents is slow
- BLAST search failed due to a change at NCBI
- Other bug fixes
Version 2.5 (13 November 2006)
Features added:
- NCBI BLAST agents
- Ability to specify advanced options to NCBI BLAST.
- Ability to change location of NCBI BLAST server.
- Sequence viewer: sequence names for alignments are now always visible (if the show names preferences on) even when scrolled to the right.
- Sequence viewer: option to display the original sequence residue position numbers in alignments and extracted sequences.
Includes displaying the original sequence residue numbers for local alignment results.
- Sequence viewer: can handle alignments of 10,000 sequences, and individual sequences up to 100 million residues in size.
Performance also improved on smaller sequences and alignments. (Documents over 100Mb only supported by Pro version).
- Geneious can handle larger documents than previous versions and displays a progress bar when loading individual large documents.
- MEGA importer
- PHRAP (ace) importer
- Genbank flat file, GBSeqXML and INSDSeqXML importers
- Export table values as CSV file.
- Improved printing support. Print preview, with various options.
- Improved saving to PNG support with preview and various options.
- Improved Dotplot viewer: Now much faster, especially for low stringency setting.
- Support importing / exporting .geneious files in zip compressed format, to save disk space.
Features added in Pro version:
- Primer design (This product includes software developed by the Whitehead Institute for Biomedical Research)
- Collaboration: Contacts can browse shared folders like their local database.
- Collaboration: Similarity (blast-like) search contacts.
- Collaboration: Chat with contacts.
- DNAStar .seq and .pro importer
- Teaching Module, allows users to create HTML tutorials for their students which link in with Geneious documents.
- Smart folders: Folders that can sort documents according to relevance to a subject.
- Can save document views to PDF and SVG images.
- Sequence viewer: can reorder sequences and remove sequences from alignments
- Sequence viewer: option to display residues the same as the consensus sequence as either "." or without any color.
- Geneious alignment can automatically detect sequence direction
- A gui interface for installing and un-installing plugins.
Bugs fixed:
Patch 2.5.4 (15 January 2007)
Bugs fixed:
- Geneious alignment crashing on sequences containing uracil (U)
- Geneious crashing on startup when two copies of the same plugin installed
- Printing on Mac OS X uses native options. Resolves several problems
Patch 2.5.3 (29 November 2006)
Bugs fixed:
- Primers in menu not working for 3 or more sequences
- Fasta exporter randomizes order of sequences in alignment
- Various stability bugs fixed
Patch 2.5.2 (17 November 2006)
Bugs fixed:
- Fixed issue where new users were not able to access a new Pro version trial.
Patch 2.5.1 (16 November 2006)
Bugs fixed:
- Fixed issue where users upgrading were not able to access a new Pro version trial.
Version 2.0 (2 August 2006)
Features added:
- New visual style and icons
- Agent interface improved
- Search interface improved
- Improved local sequence similarity search
- Additional import formats: PileUp, DNA Strider, Rich Sequence Format
- Import *.ab1 and other chromatogram files
Features added in Pro version:
- Collaboration (beta)
- Sequence editing
- Alignment editing
- ClustalW alignment
- Chromatogram viewer including sequence logos
- Open reading frame (ORF) finder
- Alignment via profile of Alignment and Sequence or two alignments
- New sequence creation
- Phylogeny tree display in alignment viewer.
- Consensus sequence in sequence viewer.
Bugs fixed:
- Alignment using excessive memory
Version 2.0.10 (4 October 2006)
Bugs fixed:
- fixed crash when exporting chromatograms
- fixed nexus tree importing bug.
Version 2.0.6 (07 September 2006)
Bugs fixed:
- fixed crash when dealing with chromatograms with no quality information
- fixed failure to import some abi (chromatogram) files.
- fixed fasta importing bug where all sequences that shared the same name would all receive the same description
- could not start up Geneiuos if the data location is invalid (drive letter changed/network drive etc.)
Version 2.0.5 (24 August 2006)
Bugs fixed:
- crash on startup after enabling direct connect option in preferences.
- tree viewer significant figures option now works for consensus.
- occasional crash on startup when loading the contents of a folder.
Version 2.0.4 (14 August 2006)
Features added:
- Support for authenticated proxy servers
Bugs fixed:
- Crashes involving chromatogram documents
- Agents retrieving documents multiple times
Version 1.2 (31 May 2006)
Features added:
- Generate consensus sequence
- Fast alignment option
- Auto detection of FASTA sequence type
- Endnote 9.0xml file support
Bugs fixed:
- Database stability improved
- Database memory leak
Patch 1.2.1 (21 June 2006)
Bugs fixed:
- documents imported from Nexus and Clustal files in 1.0 crashing in 1.2