Release notes for Geneious
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.
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