April 23rd, 2012Features:
· Restored the old annotation table view
Bugs fixed:
· Fixed "There is already a track on this sequence with name..." error message when running various operations such as cloning and SAM import
· Fixed out of memory error when viewing some sequences
· Fixed a bug where the Csv importer wasn't importing Date fields correctly.
· Fixed an error that would occur when searching a server database using a number field
· Fixed an issue with Sassafras licenses not working
April 11th, 2012Features and Improvements:
· Improved fastq import quality format guessing and added dialog asking if the guess is correct if Geneious is unsure of the format
· Better track names when running variant finding
· Batch rename can now rename multiple selected sequence list documents and multiple selected alignments
Bugs fixed:
· Fixed hang using Sequence Logo graph on big alignments/contigs.
· Sequence Viewer: Reduced memory usage when viewing lots (e.g. millions) of annotations
· Fixed occasional failure to copy documents or folders from a server database
· Fixed incorrect assembly results sometimes when mapping to a circular reference sequence
· Fixed a bug where Convert to Oligo was appending a duplicate number to the end of the Oligo's name
· Custom Blast Query-centric alignments no longer double up on annotations
· Fixed a bug that could cause primer documents in a server database to not be available in the primer chooser
· Marking a document read in a server database no longer completely re-indexes it
April 11th, 2012Parent-Descendant tracking:
· Sequences can be actively linked to each other as parent/descendants. Active links are created by all cloning related operations.
· When a parent sequence is edited, Geneious can propagate the changes to all actively linked child sequences, save the changes to a copy or deactivate the links.Pro-only
· Documents can also be inactively linked to each other which means there is a record of their relationship but changes cannot be propagated. All non-cloning operations create inactive links.
· New lineage view shows parent and descendant relationships, including active and inactive links and the operations that where performed.
Sequence View Improvements:
· Added 'By Direction' color scheme for coloring sequencing reads based on their direction
· Statistics show mean forward/reverse coverage of the selected region Pro-only
· Improved performance when viewing contigs with regions of very high coverage (e.g. 5,000+)
· Separated "Find in annotations" and "Find in Sequence Names" options to allow efficient annotation searching on big contigs
· Improved performance viewing big contigs with annotated reference sequences
· Can edit the color of individual annotations Pro-only
· Translation now displays both amino acids for ambiguous codons that translate to 2 possible amino acids
· Go to base now uses the un-gapped position for the reference sequence in assemblies
New annotation table:
· Allows bulk selection, deleting and editing of annotations Pro-only
· Improved performance on large data sets Pro-only
· Remembers column state between documents Pro-only
· Integrated with sequence view so it shares all the same controls Pro-only
Variation/SNP Finder Improvements:
· Added 'Minimum Strand-Bias P-value' setting for reducing false SNPs due to sequencing error Pro-only
· Better identification of tandem repeat amplification/reduction Pro-only
· Track names added to the reference sequence now include the sample name in the track name Pro-only
· Added "CDS Codon Number" field to indicate which codon in the CDS the SNP applies to Pro-only
· Added "CDS Position Within Codon" field to indicate which position within a codon (1, 2, or 3) in the CDS the SNP applies to Pro-only
Other New Features:
· New Align/Assemble menu replaces the separate Alignment and Assembly buttons to make it easy to choose the correct algorithm
· De Novo Assembly: Reduced memory usage, improved performance and more accurate memory usage estimates
· Improved performance importing fasta/fastq/sam/bam files
· Files that are copied from the desktop can now be pasted in to the document table or imported using Import - From Clipboard in the File menu.
· Primer Trimming: Improved performance (about 7 times faster) Pro-only
· Primer characteristics can now be used for reverse primers and primer pairs Pro-only
· Test with Saved Primers now records mismatch locations as annotations and in a new qualifier Pro-only
· Extract button added to Sequence Lengths Graph Pro-only
· Strip alignment columns can now strip columns containing a certain percentage of gaps Pro-only
· Enzymes view is now available when more than one sequence is selected Pro-only
· 2D DNA fold viwer added which is available on any nucleotide sequence under 3000bp in length Pro-only
· Distances view now has # Differences and # Identities matrices Pro-only
· Plugin Development/Public API: Improved documentation
· When generating consensus trees, they can now be saved to a separate document.
· Can sort documents by their color (new color column added)
· Server Database: Improved performance
Bugs fixed:
· Reduced memory usage on long-lived databases by storing preferences more efficiently
November 7th, 2011Bugs fixed:
· Sequence Search: Fixed crash sometimes when doing a sequence search
· Sequence Viewer: Fixed crash after deleting sequences in genome lists
· Sequence Viewer: Fixed hang/crash when resizing some trim annotations
· Sequence Viewer: Fixed crash clicking 'go to next annotation' button on some restriction site annotations
· Sequence/Contig Viewer: Fixed crash if you delete a track, create one with the same name, and click save
· Sequence/Contig Viewer: Fixed crash when loading a document that previously had an annotation selected in a track, but that track was turned off while viewing another document
· Alignment/Contig Viewer: Fixed not rendering SNP/coverage annotations on the reference sequence that lie past the ends of the reference sequence
· Alignment/Contig Viewer: Fixed it saying you need to zoom in to view reads on contigs that only have a few reads
· Alignment/Contig Viewer: Fixed occasional crash when dragging bases/gaps around during alignment editing
· Alignment/Contig Viewer: Fixed out of memory crash sometimes when saving new tracks
· Alignment/Contig Viewer: Fixed crash sometimes when removing chromatogram sequences from a contig
· Assembly: Fixed crash in some cases when mapping a contig to a circular reference sequence. And improved results so that contigs spanning the origin map individual reads to both sides of the origin
· SNP Finder: Fixed crash on some data sets.
· SNP Finder: Fixed it incorrectly reporting 'no protein effect' when there is a deletion or insertion that doesn't change the amino acid at that point
· SNP Finder: Fixed it not reporting results correctly when there are overlapping CDS annotations
· SNP Finder: Fixed it not reporting results when choosing to find in CDS annotations only with 'analyze effects on translation' off
· SNP Finder: Fixed p-value missing from results in some cases when using exact p-value calculations
· Set Paired Reads: Fixed crash when pairing multiple sequence lists by linker.
· Set Paired Reads: Fixed crash when repairing reads with mixed relative orientations.
· Annotations table: Fixed very slow sorting
· Annotations table: Fixed occasional crash when no longer viewed
· Primer Design: Fixed a bug where sequences designated as probes were showing up with a forward primer annotation instead
· Primer Design: Fixed a bug where the salt concentration was not being taken into account when calculating TM of primers
· Primer Design: Fixed a bug where calculating characteristics was failing on multiple selections
· Fixed crash sometimes when deleting a folder
· Search index: Fixed crash sometimes when building search index for contigs with tracks
· Made changes to NCBI BLAST to adhere closer to the guidelines given by NCBI. Geneious will not hit NCBI limits as easily. Also removed the 11kbp sequence length constraint from BLAST searching.
· Ace exporter: fixed a bug where it was exporting gap qualities
· Fixed major crash under Java 7
· Fixed issue where Geneious reports incorrect codon_start on CDSs on documents downloaded from NCBI which have foreign intervals
September 20th, 2011Sequence View Improvements:
· New annotation track functionality that groups annotations from a common source so they can be rearranged, colored, shown/hidden, deleted etc Pro-only
· Added an interactive mini-map that shows your current position in the genome and a summary of annotations
· Added a real-time annotation filter in the annotation controls Pro-only
· Added a chromosome selector when viewing an entire genome as a sequence list (saves memory and improves performance)
· Added a slider for changing the zoom level on genomes
· Redesigned "go to position" to have a single input field and a shortcut button in zoom controls on genomes
· Annotations are arranged more efficiently on genomes
· Positions in big sequences are now rendered like 45.2 mb instead of 45,200,000
· Added ability to extract multiple primer annotations simultaneously
· Annotation generators can now run on more than one alignment simultaneously. Eg. "Find Variants/SNPs" Pro-only
· "Add Annotation" button can now create separate annotations for each selected region Pro-only
· Coverage graph: Added logarithmic scale option and added mean coverage indicator on scale bar.
· Can click on annotation types in the controls to change all annotations of that type to a new type Pro-only
· Added "Copy (reverse complement)" to right-click popup menu
Other new features:
· New One Step gateway operation that does BP and LR reactions in one step Pro-only
· New Download Annotation Tracks operation to annotate genomes with data from Broad Institute Pro-only
New CSV/TSV Importer:
· Import primers, probes and nucleotide/amino-acid sequences from spreadsheets
· All operations can now have their setting saved to a profile for re-using later or sharing with other people Pro-only
· New Support button that makes it easier to contact our support team and attaches system information so we can answer you more efficiently
· New 'Compare Annotations' operation to compare annotations of different types on a sequence Pro-only
· Primer Testing: Can now test a selection of primers from your database Pro-only
· New graph view displaying distribution of paired read distances in a contig Pro-only
· Distances viewer now works on alignments and can display a percent identity matrix (plus other small improvements) Pro-only
· Share Geneious documents and visualizations with your friends and colleagues via Email, Twitter or Facebook
· New TSV (Tab separated values) exporter
· Import sequences by pasting straight in to Geneious
· New checkbox column in table makes it easier to select multiple documents (no key presses required)
· SAM/BAM importer
· Improved performance and progress reporting
· Groups unmapped sequences by reference when known
· Can import more than one SAM/BAM file at once
· Find Variations/SNPs improvements Pro-only
· Added option to specify what properties of CDS annotations to copy to SNP annotations. Added CDS interval number property to SNP annotations
· Added p-value to variations and added a maximum p-value threshold for finding variations. This fixes incorrect variations reported around 454 homopolymer regions
· Added option to find variations within the sample (rather than comparing to the reference sequence)
· Ambiguities characters are now interpreted instead of being treated as different character types
· Assembly improvements Pro-only
· Better results when assembling to large reference genomes
· Added setting to save used reads (and optionally their non-mapping mates)
· Increased maximum reference sequences from 10,000 to 25,000 and added Preferences->General->Advanced->Assembly.maxReferenceSequences to increase it further (although this is not recommended as performance will be poor)
· Added 'Map multiple best matches' setting (for unpaired reads only) to read mapping/reference sequence assembly
· Added 'Assemble each sequence list separately' setting for performing multiple assemblies in one step
· CSV export can now include complete sequence
· Chromatograph View: Highlights the selected region from the sequence view
· GFF importer imports GTF format
· GFF importer more memory-efficient
· Strip alignment columns: can now strip every third position or columns containing one or more gaps Pro-only
· Transfer annotations: Added option to transfer annotations to the consensus sequence Pro-only
· Annotations table: Minimum, Maximum and Length columns values no longer include gaps in calculation. Added new columns with the old values Pro-only
· Annotations table: Added horizontal scrollbar and auto-size width of columns Pro-only
· Annotations table: Enhanced performance and fixed hangs when sorting or filtering extremely large numbers of annotations Pro-only
· Set Paired Reads: Added option to pair reads by name and now handles missing reads Pro-only
· Concatenation can now add NNNNN spacers between sequences Pro-only
· New column on contigs and alignments that displays the reference sequence name
· GenBank Flat importer now copes if there's no locus
· Now possible to import CAF file(s) and other file(s) simultaneously
· FASTA exporter can limit lines to 80 characters
· ClustalW is now bundled with Geneious Pro-only
· Added ability to release floating license Pro-only
Bugs fixed:
· Fixed partial CDS annotations (which include only a subset of the full CDS intervals) displaying out of frame annotations when extracted from a document containing the complete CDS
· Fixed deletion annotation at end of sequence not being displayed in sequence viewer
· Batch rename now offers Description of the sequences in an alignment as a readable field when renaming
· Primer characteristic calculation including during oligo import from VectorNTI much faster
· Fixed crashes when alignment engines like MUSCLE and ClustalW return no alignment or unexpectedly return a local alignment
· Reduced memory usage required to move large documents from one folder to another
· Sequence similarity statistics respect trim annotations better
· Improved speed of FASTA im/exporter
· Improved speed of Find Duplicates
· Decreases memory usage of "Extract sequences from list"
· Avoided hang when adding custom BLAST database which produces lots of errors from formatdb
· Stopped GenBank exporter adding name label to features in unmodified documents
· Fixed crash when extracting contig from contig and some sequences in the extract region consist entirely of gaps
· Made Gateway Cloning cope with sites over origin when sites are attX1 and attX2; better error message for multi-site
· Stopped dialog popping up repeatedly if support on your permanent license expires while Geneious is not running
· Geneious now deletes file results from cancelled backup
· Fixed crash in RNAFold when output in unexpected format
· Fixed crash in SAM importer when file contains unaligned records without base sequence
· Fixed crash in SAM importer when encountering the X operator
· Fixed crash in download from NCBI when mandatory element missing
· Stopped ClustalW importer potentially importer alignments with mixture of nucleotide and protein sequences
· Stopped Custom BLAST losing document fields such as organism
· Stopped VNTI import crash when different molecules have custom fields with different fields
· Improved performance when editing bases in a genome
· Stopped Geneious assembler falsely identify regions in large genome as repetitive (and not mapping reads there)
June 30th, 2011Bugs fixed:
· Fixed changes being lost when making changes to an alignment built from a sequence list
· Fixed occasional crash exporting in SAM/BAM format
· Fixed crash that can happen downloading full documents from a tblastn run
· Fixed bug that can cause sequences extracted from tree document to be in the wrong order
· Fixed crash that can occur importing ACE files with reads starting or ending with gaps and having trimmed regions
· Removed possibility of crash from removing invalid bases from sequences with quality/traces on import
Pro-only features now enabled in Geneious Basic:
· All import and export
· Visualisation including circular sequences, chromatograms, color schemes, translation, highlighting, dotplot etc
· Teaching tutorials
· Save as PDF and SVG
· NCBI Gene and SNP databases
· Alignment options
June 7th, 2011New features:
· Added "Whole Words Only" checkbox to local documents searching so that you can search for partial words
· Added "Find All" button when using "Find in Document" on the sequence/alignment viewer
· Can select multiple folders for moving/deleting and for showing the contents of them all at once
Bugs fixed:
· When a sequence is circularized, annotation intervals extending past the ends of the sequence are now truncated
· When a sequence is de-circularized, annotation intervals spanning the origin are split into multiple intervals
· Fixed poor performance when viewing some sequences with over 100,000 annotations
· Empty sub-folders are now kept when exporting folders
· Separate by barcode works on already paired reads and lets you choose which sequence in the pair has the barcode
· Fixed problem with garbled fonts on some systems
· Fixed de novo assembler running out of file handles on machines with lots of processors
· Greatly improved the speed at which Geneious performs large batch BLAST searches
· Fixed crash when loading some contigs (which would also cause search index to crash)
May 12th, 2011Bugs fixed:
· Fixed extra highlighting showing up when highlighting disagreements in the translation of a nucleotide alignment
· Fixed out of memory crash when selecting a big sequence list or contig while the fasta viewer plugin is enabled
· Fixed crash when importing sequences which contain invalid nucleotide or amino acid characters
· Fixed "fromKey>toKey" crash when importing SAM/BAM file
· Fixed crash importing SAM/BAM file when soft clipped region overhangs the start of the reference
· Fixed crash adding enzymes to set
· Improved trimming performance
· Improved SAM/BAM import performance when importing file with multiple references
· Modified Gateway to support use of destination vector with multiple attR pairs
· Fixed queuing misbehaving on a FLEXnet floating license with multiple seats
· Fixed crash extracting from alignment where sequences have been deleted
· Fixed crash during re-assembly if the input contig which contains a reference sequence has sequences that don't overlap the reference sequence
· Fixed crash when extracting zero length annotation from annotations table
· Fixed .fq extension file not being recognized as fastq
· Fixed possible issues wih file handles when importing many small contigs from ACE or SAM/BAM files
April 28th, 2011Bugs fixed:
· Reduced excessive memory usage by Nexus exporter
· Reduced excessive memory usage by fasta custom BLAST database adder
· Fixed crash when exporting sequence to SAM file with < 2 characters in name
· Improved performance of trimming
· Fixed crash creating Pfam documents using Pfam 24
· Fixed crash when trying to create an aligment of 1 sequence only
· Fixed crash deleting or changing reference sequence in big contigs
· Fixed incorrect amino acid and codon usage statistics after manually editing CDS annotations
· Fixed crash due to too many open files when dealing with large sets of contigs
April 19th, 2011New features:
· Added support for NCBI genetic codes 16, 21, 22 and 23
· Enabled Chromatogram view by default and improved user interface
· Made split view on a circular sequence not rotate the view when at minimum zoom when synchronizing the selection with another view
Bugs fixed:
· Fixed bug in Variant/SNP finder where positions with multiple variations from the reference sequence were incorrectly labeled as insertions.
· Fixed bug where searching for a sequence name or annotation or sub-sequence that start on the first base of a sequence were sometimes being incorrectly reported as not found
· Fixed some performance issues with large contigs
· Fixed GC graph frame plot offset by 1 base in some positions
· Fixed crash when trimming some sequences
· Fixed crash when reference assembling trimmed sequences
· Fixed crash creating editable copy of blast results
· Fixed paired reads becoming unpaired when editing a contig or sequence list
· If a sequence includes its genetic code (e.g. genbank sequences usually do), the sequence viewer now uses that as the default genetic code in the translation options
· Fixed translation giving incorrect first amino acid on some translations (e.g. for the standard genetic code, CTG should translate to M instead of L when it is the first codon)
· Adjusted NCBI structure viewer to adapt to changes at NCBI's end
· Improved error messages in Gateway Cloning
· Fixed Geneious sometimes crashing (not caused by doing anything in particular)
· Fixed a bug that would cause a progress window to stick around when connecting server databases on start up
· Fixed crash that occurred when deleting documents while having multiple server database folders selected
· Fixed hang when viewing sequence lists containing long sequences
· Fixed Geneious crashing when running out of disk space
· Fixed crash when circularizing some sequences
· Fixed a crash that would sometimes occur when resuming a BLAST search
· Fixed a crash when clicking on consensus sequences annotations that extend outside the bounds of the alignment
· Fixed bug during large contig creation in 5.4.0 where contigs were prone to crashing later and had performance problems when viewing them
· Added progress to pfam operations
· Fixed issues with some file import terminating early
· Stopped ability to export files with characters in them that were not legal in filenames
· Fixed crash when using GFF or BED importer to annotate certain sequences
· Added a trial
· Fixed odd behaviour in SAM/BAM exporter when document contains a mixture of paired and upaired reads
· Fixed crash in PopSet when downloading a document that has no date
· Stopped export of GenBank sequences using wrong XML type for Seq_other-seqids field
· Fixed concatenation of protein sequences
· Decreased memory usage when downloading long sequences from GenBank
· Made Newick importer more memory-efficient
· Fixed issue affecting Mafft alignments of RNA
· Fixed crash when extracting from an alignment where the reference sequence is not the first sequence
· Fixed bug where a reference sequence could be assigned to an extracted alignment even when there is none
· Fixed issues where extracted alignments could contain sequences consisting only of gaps
· Fixed slow performance viewing some contigs
· Fixed very slow performance (hang) when editing some big alignments/contigs
· Fixed crash when trying to import more than one SAM/BAM file at once
· Fixed hang when selecting similarity or by annotation color scheme on large contigs
· Annotation Table now displays trimmed regions on all sequence lists
· Annotation Table now displays annotations from both views of a blast hit
· Improved dotplot view initial loading time
· Fixed issue with reordering of sequences with overhangs not being respected during concatenation
March 14th, 2011· Fixed a frequent crash that was introduced into the server database with v5.3.5
March 14th, 2011Bugs fixed:
· Fixed crash when using "Find Variations/SNPs" on contigs with trim annotations
· Fixed MySQL 5.5 compatibility issue in Server Database
· Improved SOLiD csfasta import to include [.456] characters
· Fixed issue preventing the addition of custom NCBI databases
· Fixed bug in licensing when migrating hard drive
· Fixed issue where users on 64-bit Windows could not activate a license using 32-bit JRE
December 30th, 2010Bugs fixed:
· Fixed crash in the Annotation table viewer"
· Fixed a crash in the GFF3 importer when parent is in a different sequence to child
· Fixed SAM Importer problem where reads were being imported offset from their correct position
· Fixed misc. licensing activation issues
November 9th, 2010Bugs fixed:
· Fixed failure to search UniProt databases due to change on UniProt servers
· Fixed a crash that could occur when importing a SAM file
· Fixed crash that could occur when deleting trimmed regions from reads
October 19th, 2010Bugs fixed:
· If you grouped sequences into a list then edited the sequences in the list in the sequence viewer, changes could get lost when restarting Geneious
· Fixed crash during NCBI search that starting happening due to a change at NCBI's end
· Fixed crash on startup that would disable Sequence Search
October 14th, 2010Bugs fixed:
· Fixed crash when assembling contigs that have trim annotations
· Fixed 'assemble by name' appending 'Contig' to the names of all generated contigs when saving results in sub-folder
· Fixed 'assemble by name' with empty assembly name prefixing contig names with numbers
· When assembling a few sequences the default was 'Highest Sensitivity' but if you didn't change it, it would do a 'Medium Sensitivity' assembly
· Fixed off-by-one error in annotations in GFF files with a sequence-region
· Fixed "No enzyme called... " occurring for some users when viewing nucleotide documents
· Fixed crash in SAM importer when cancelling from reference sequence file chooser
· Fixed crash displaying options when using "Insert into Vector" with an isnert sequence with very long overhangs
· Fixed persistent crash on startup when some one-month student licenses expired
· Fixed incorrect concatenation when a fragment had an extracted region that did not cover the entire fragment
· Fixed an issue where documents that contained non-ASCII characters could not be added to or retrieved from a Microsoft SQL Server database
· Fixed occasional crash in RNA Fold viewer
September 30th, 2010Bugs fixed:
· Fixed crash when viewing folders containing alignments or trees for some users
· Fixed crash selecting 'Transfer Annotations' in the sequence view of a BLAST hit
· Fixed crash when importing some unusually named sets of sequences
· Fixed assemble by name appending 'Contig' to the names of all generated contigs
· License activation uses port 80
· Fixed crash when doing tblastn
· Fixed crash importing ace file where first base in consensus is a gap
· Offer to replace end gaps with Xs when fasta exporting protein alignment
· Fixed GFF importer's base numbering off-by-one error
· "Design with Existing" for Primer Design no longer disabled when it shouldn't be
· Fixed an issue where Geneious could stay blank for a while after performing a full back up
· Fixed GUI hang when deleting jobs from remote services in operations table
September 22nd, 2010· Fixed crash when trying to assemble blast results
· Fixed crash when deleting documents from the hit table of sequence search results
· Fixed crash when reference sequence assembling with 'Save contigs' turned off
· Fixed crash extracting manually-created primers from sequences
· Fixed crash digesting plasmid created from fragments with and without quality
· Fixed crash importing SAM file where soft clip overlaps consensus
· Fixed local blastx
· Fixed issue where fasta files are detected to be artemis files
· Removed uss of -stable flag in MUSCLE
· Progress window is now displayed immediately when adding a custom blast database
September 15th, 2010New features:
· Can delete local and remote jobs in Operations table
Bugs fixed:
· Reduced memory usage when doing reference sequence assembly
· Fixed bug where the number stating how many restrictions sites were found was incorrect
· Fixed crash sometimes when removing trimmed regions in alignment view
· Fixed crash when assembling a contig to a reference sequence
· Fixed odd behaviour in collaboration when two users start a chat to each other simultaneously, or one disconnects and reconnects
· Fixed bug where multiple single-user licenses bought as a batch were detected as the same license
· Tweaks to whitespace in GenBank flat exporter
· Fixed crash displaying Options in Document History if the plugin that created the Document is uninstalled
July 15th, 2010Bugs fixed:
· SAM importer 30 - 50 times faster
· Fixed a few small bugs in SAM importer
· Better progress for custom BLAST and ClustalW alignment
· VNTI importer can import files with empty motifs, subbases with characters illegal in file names, and notes with different fields to existing ones
· Fixed trimming incrrectly annotating primer and vector hits when trimmed regions are removed
· Pir importer can import files using dot as gap chracter
· Fixed hang when Geneious regains focus on Pfam panel
· Fixed occasional crash when selecting a region in the sequence/alignment view
· Fixed compatability with Microsoft JDBC driver
· Addressed issues with large option windows on low resolution screens
· Notes can now be shown on tips in the tree view again
July 9th, 2010New features:
· Can have the pipe character "|" displayed for identities in the text view for pairwise alignments and blast hits (Advanced options in General Preferences)
Bugs fixed:
· Fixed crash sometimes after saving changes to a contig or alignment
· Fixed sequence/contig/alignment viewer displaying the original name instead of the current name for some sequences.
· Some icons were missing when running Geneious using Java 5
· Generating a consensus sequence from a contig ignored the 'Assign Quality' setting if the reference sequence had no quality
· Fixed crash during de novo assembly of sequences containing too many ambiguities
· Fixed a bug in the generation of assembly reports when assembly from existing contigs
· Sequences with quality but no chromatogram trace no longer have the chromatogram icon (eg. extracted consensus sequences)
· Fixed crash when concatenating or ligating some types of sequence list documents.
· Fixed sequence viewer not displaying some graphs (e.g. CpG Islands) because it wrongly thought the sequence had been edited
· Extracting a sequence can no longer result in partial restriction sites or primer binding sites
· Fixed annotations appearing 1 off from their correct location when extracting a region from an alignment starting with a gap
· Fixed a bug that caused to appear in the export of BLAST alignments in traditional BLAST text format
· Fixed crash aligning a sequence consisting entirely of gaps
· Improved memory efficiency, progress reporting and cancellability of the SAM importer
· Fixed GenBank importer to recognise recognition sequences on enzyme annotations exported from Geneious
· Fixed crash concatenating sequences containing quality but no traces
· Insert into Vector recognises cut sites that have amibiguities or have direction when they shouldn't
· Better error reporting for FLEXnet licenses including trials
· Vector NTI importer ignores files starting with ._
· Fixed local documents reindexing your entire database sometimes when you restart Geneious before it finishes indexing
· Extract PCR Product now works on sequences where primer annotations are right on the end.
· Fixed the alignment of text in the blast text view on certain systems
April 19th, 2010New features:
· Can now re-root rooted trees in Tree View
· View preferences can now be stored separately for each document in the sequence view
· New controls layout in the sequence view
· Fragment length is shown when one restriction site is selected and the mouse is moved over another in the sequence view
· Added buttons and shortcut keys to the sequence viewer to go to the next/previous annotation of the same type
December 18th, 2009New 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.
November 30th, 2009Bugs fixed:
· Fixed a bug that caused Smart Agents to become normal agents after restarting Geneious
· Reduced memory usage for sensitivity based denovo assembly
November 30th, 2009Bugs 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
October 29th, 2009New 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
September 23rd, 2009Bugs fixed:
· 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
August 7th, 2009· 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
June 30th, 2009New 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
June 30th, 2009· 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
December 22nd, 2008· 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
July 19th, 2008· Fixed crash when encountering invalid NCBI files which have no division
May 8th, 2008New 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.
March 26th, 2008· 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)
December 19th, 2007· 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
November 26th, 2007· 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 Sequecne -> 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.
· Improved dot plot - Added a crosshair
· Sequence view improvements - Graphs now stay in view always and the names are resizable.
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