Release notes for Geneious

Version 6.1 (7 February 2013)

• Primer Design
  • New cloning primer design task added for designing primers with fixed 5' binding positions
  • Repeat library mispriming added to avoid binding to known repeats
  • Primer extensions can now be chosen from the primer design options
  • Designed primers now have nicer names
• Sequence View
  • When adding or editing annotations you can choose which track they are on.
  • Replaced the "Move all of annotation type" option with a more general "Edit all of annotation type" option.
  • Added right click option to copy a sequence name or other displayed field.
  • Removed restriction on maximum length of text that can be searched for as long as interpreting ambiguities is turned off
• Alignment/Contig View
  • Added option to hide columns with more than X% gaps
  • Can drag select the alignment numbering to select all sequences in alignments/contigs
  • Added find dialog option to allow gaps between characters being searched for
  • Improved rendering performance (5 times faster in some cases)
• Custom BLAST now supports BLAST+ (existing users will have to upgrade blast manually, new users get BLAST+ by default).
• Back Translate now has codon usage tables for producing unambiguous nucleotide sequence (uses EMBOSS tool backtranseq)
• DNA/RNA fold view now available on two sequences, showing how the two molecules bind to each other (uses Vienna rnacofold 2.0.7)
• DNA/RNA fold view updated with new stats panel, better probability color scheme and new energy models
• High/Low Coverage Finder: Added option to merge annotations less than a specified number of bases apart.
• More things are multi-threaded which makes them faster (e.g. trimming, read mapper indexing)
• De Novo Assembly: Slightly better results on gappy data
• Lengths Graph: Added option to display contig lengths
• New "Grade" column for sequence search results that combines E-value, identity and query coverage in to a single percentage
• Cut positions in enzyme table viewer split into count and positions for easier sorting
• Lambda PFG, Low range PFG and Lambda DNA-BstEII ladders added to virtual gel view
• New geneious.properties file can be used by admins to configure geneious
• Text View now available when several documents are selected
• New Bowtie2 assembly option added on Geneious Server

Bugs fixed:

• Circular contigs now correctly render graphs (e.g. chromatograms) on sequences that wrap past the circular origin
• Fixed a crash when importing primers from csv of longer than 36bp

Additional Notes:

• Sample documents have been changed significantly
• The Solaris operating system is no longer supported officially
• Most text is now rendered clearly on Retina display macs
• Trial licenses now have to be requested and activated
• Vienna rnafold updated to 2.0.7
• All EMBOSS tools updated to 6.5.7
• Bowtie updated to 0.12.8 (Geneious Server)
• SOAP2 updated to 2.21 (Geneious Server)

Patch 6.1.1 (27 February 2013)

New features:

• Sequence Viewer: Can revert editing annotations (Insertions, Replacements, Deletions)

Bugs fixed:

• Alignment Viewer: Fixed crash when searching for long text on alignments with the 'Allow extra gaps in sequence' setting on
• Alignment Viewer: Fixed crash when clicking on annotations in pairwise alignments when the consensus sequence is off
• Contig Viewer: Fixed it incorrectly scrolling down when zooming in sometimes
• Contig/Alignment Viewer: Fixed hangs when deleting large selections. Also improved deletion behaviour to replace non-gaps with gaps when deleting
• Stop crash when starting up when data is stored on an unmounted network drive
• Fix issue where queueing for already-queued FlexNet license would stop you from getting the license when it came available
• Fix potential hang on shutdown (due to preference clearing issue)
• Stop sequences imported from VNTI's .gb format having "(modified)" appended to the name
• NCBI BLAST available in restricted version again
• Fix crash in feature finder when searching for features annotated on reverse of protein sequence
• Improvements to queueing behaviour of FlexNet and Sassafras floating licenses
• Nexus importer now importing attributes as document fields
• Fix crash in BAM exporter when multiple documents have same name
• Fix off-by-one error in Gateway annotator which could lead to crashes in Gateway operations
• Clipboard Csv/Tsv import now offers you the choice of which of the two formats to import as. Previously it would erroneously choose the first format which was well-formed.
• Fixed a bug where too many excluded regions were being sent to primer3 when primer design was run on some alignments
• Made several consistency changes when importing/creating primers that were too short or too long for primer3, across several tools
• Fixed a crash in Primer testing when a match on a circular sequence with mismatches fell over the origin

Additional Notes:

• BWA updated to 0.6.2 (Geneious Server)
• Velvet updated to 1.2.08 and Velvet optimizer updated to 2.2.5 (Geneious Server)

Patch 6.1.2 (4 March 2013)

Bugs fixed:

• Fixed Primer design with existing crash when existing primer doesn't match target sequence perfectly
• Removed ability to make shortcuts to system operations
• Fixed bug in PopSet full document download affecting number of results
• Fix issue with Gateway operations where the AttX1 site straddled the origin
• Fix issue with Sassafras licenses not releasing properly when released through Pro menu

Geneious Server:

• Streamlined Geneious Server installation procedure
• Under the hood changes to harden security in admin console

Patch 6.1.3 (25 March 2013)

Bugs fixed:

• Contig Viewer: Fixed poor performance viewing large contigs with many hidden columns of gaps
• Contig Viewer: Fixed reordering of sequences getting lost when saving on some contigs
• Contig Viewer: Fixed incorrect translation on reads in circular contigs that wrap past the origin
• Sequence Viewer: Fixed missing position labels at the ends of selected annotations sometimes and fixed incorrect position labels when resizing annotations
• Sequence Viewer: Fixed paired reads being paired incorrectly after deleting sequences
• Sequence/Contig Viewer: Fixed hang when deleting lots of sequences
• Sequence/Contig Viewer: Fixed crash sometimes when deleting trim annotations
• Sequence/Contig Viewer: Fixed crash and/or incorrect results when annotating or trimming multiple sequence lists after first sorting the sequences inside them
• Fixed a bug where Sequence Searches that were running at the time of upgrading to 6.1.0 would crash on startup
• Annotations Table: Fixed incorrect length of annotations crossing the origin of circular sequences
• Fix crash importing Nexus documents
• Fix unresponsiveness when running Modeltest from the PAUP* plugin
• Fix a crash that could occur when custom BLAST gives back results in unusual format
• Fix rare crash in Feature Finder
• Read Mapper: Fixed crash in rare situations when using iterative mapping
• De novo assembly: Fixed poor results in some cases when de novo assembling 454/Ion Torrent data
• Stop Geneious automatically checking Sassafras license out again when it is manually released
• Fix issue with BLAST+ only reporting 100 hits when searching for more than this
• Fix hang shutting down Geneious when there is blocked multicast socket

Patch 6.1.4 (9 April 2013)

Bugs fixed:

• Reference Assembly: Fixed incorrect handling of RNA data
• Reference Assembly: Fixed mapping results being offset from where they should be sometimes
• Coverage Graph: Fixed it being slightly offset from where it should be when hiding columns of gaps
• DNA/RNA Fold viewer: Fixed crash on some pairs of sequences
• Variant Finder: Fixed crash in rare cases when calculating p-values
• De novo Assembly: Better results on data with homopolymer style error models (e.g. Ion Torrent or 454)
• Fix issue where quality ended up on the wrong bases when concatenating a mixture of quality and non-quality sequences
• Fix issue where it was not possible to use GreenButton and a FlexNet license server at the same time

Geneious Server:

• Fix issue with PAUP* not running on Geneious Server

Patch 6.1.5 (13 May 2013)

Bugs fixed:

• Sequence Viewer: Fixed it incorrectly scrolling down sometimes when drag-selecting regions
• Sam importer: Fix issue with read positioning in reads with a soft clip overhanging the start of the reference
• Shared Database: Fixed primers in shared databases not showing up in primer testing options sometimes
• Variant Finder: Fixed incorrect amino acid effects for variants on left directed CDS annotations where only the first and third position in a codon have varied
• De Novo assembly: Fixed hang when running on documents in a shared database
• Read mapping: When mapping reads containing ambiguities with the option turned on to map them to all matching locations, it could sometimes map a read multiple times to the same location.
• Reverse complementing sequences containing variant annotations now correctly reverse complements appropriate properties of the variant annotation
• Set paired reads: Fixed default direction indicator image showing forward/forward instead of forward/reverse
• "Other arguments" option in custom BLAST now working for BLAST+
• Fixed various issues that could occur when Geneious or plugins installed on a path with non-ascii characters (eg diacritics)
• Fixed "Bin into 'Has hits' vs 'No hits' when using BLAST+
• Fixed incorrect chromatogram and identity graph rendering when using the 'Hide columns over x% gaps' setting.

Version 6.0 (4 October 2012)

• Primer Design and Testing
  • primer3 upgraded to version 2.3.4
  • Hairpin and dimer characteristics now calculated as melting point (Tm)
  • Design on sub-region of a long sequence is much faster
  • Updated melting point calculation parameters
  • Primer testing performance improved
  • Selecting two nested regions (by holding ctrl/cmd) in the sequence view will now set the included and target regions
• Sequence/Alignment/Contig Viewer:
  • Reference sequence floats at the top like the consensus sequence
  • Can choose to number just the alignment without also numbering the reference sequence
  • Annotations with db_xref links and from dbSNP are now hyperlinked to relevant web site entry
  • Statistics display the percentage of bases that are at least quality 20, 30 and 40.
  • Added option to change the thickness of annotations
  • Nicer positioning of annotation labels
  • Can edit properties (e.g. description) of sequences in sequence lists and alignments
• Improved support for read mapping when choosing to map reads to multiple locations:
  • Coverage graph and find high/low coverage weight reads less based on the number of locations they map to
  • Variant finder and consensus sequence generator: Added option to ignore reads mapped to multiple locations
  • Reference assembler supports using the "map reads to multiple locations" on paired reads
  • Contig Viewer: Added '# Mapped Locations' color scheme
  • Contig Viewer: Status bar indicates number of locations the read is mapped to.
  • Assembler has new option to not map reads at all that would otherwise map to multiple locations
• Variants Finder:
  • Added option to include the sequence names contributing to each variant in the annotation
  • Added 'Homopolymer quality reduction' setting to assist in eliminating false variants
  • Amino acid changes reported now take into account variants elsewhere in the codon
  • Added 'Average Quality' property on annotations
  • Extended option limiting variations to within annotations of a particular type to also allow finding variations within a specified range of those annotations
• Import/Export:
  • Added VCF import
  • Added support for publishing figures to SWF and EMF
  • Added ability to import SAM/BAM file against subsequence of reference
  • Fastq import can import multiple files with same quality settings
  • Geneious can now import files that have been zipped or gzipped
• Assembly:
  • De Novo Assembly: Added option to only use percentage of input data for better performance when you have too much data
  • De Novo Assembly: Improved assembly results
  • Reference Assembly: New fine tuning algorithm that generates much better results, is faster, and generally uses less memory
• Extraction:
  • Extraction, reverse complement and translate have document history
  • Fixed issue where extension ended up at wrong end of primer extracted from reverse strand
  • Added 'Complement Only' and 'Reverse Only' operations (this is not in default distributions - it needs to be installed from the plugins window)
  • Extract Annotations now lets you choose what other annotations from sequences are included in extraction
• New Feature Finder automatically annotates plasmids and other sequences with database of features
• Annotations Table in separate tab now supports editing
• Sequence/Alignment/Annotations Viewers: Filter box now provides more powerful field-based filtering
• Forwards compatibility. Geneious 6 will be able to handle most documents that people export or put in shared databases using future versions.
• Circular reference sequence assemblies: Contig viewer displays them correctly and consensus calling, variant finding and high/low coverage finding and statistics correctly handle them
• High/Low Coverage Finder: Nicer track names for contigs with reference sequences (like the variant finder has)
• Consensus: When the reference sequence has no coverage, you can now choose to call either ?, N, Gap, or the reference sequence value
• Find Duplicates operation gives option to create new sequence list containing duplicates
• Modified date field is no longer updated on documents used as input to operations
• GenBank "contig" download downloads the full document and not the documents that comprise it
• Sequence Search: Now automatically ignores leading and trailing trim regions
• Full screen now supported on Mac OS X Lion and above
• Improvements to transcription factor search output: Transcription factor name, clickable link out to Tranfac entry, explanation of quality values.
• New "Info" view tab which contains Lineage, History and Properties. Properties combines the previous "Notes" view with the ability to edit common fields like Description and Organism
• Shared Database: Folders that a user cannot view are now hidden by default. They can be shown again by right clicking on the root database folder.
• Tree viewer now shows consensus support just above nodes
• Profile Alignment plugin turned off by default
• Collaboration menu moved under Tools menu
• Lots of other little improvements

Bugs fixed:

• Sequence Viewer: When zoomed out, adjacent annotations looked like they were overlapping
• Editing 'Topology' field directly instead of changing it via the Sequence menu didn't work

Additional Notes:

• Geneious is signed on Windows and MacOS. This means it can be downloaded from Internet Explorer 9+ without warning and Gatekeeper will not reject it.
• Geneious now requires Java 6. Geneious will no longer run on Java 5. This means Geneious will no longer run on platforms where Java 6 is unavailable such as Power PC Macs and Mac OS X 10.4 (Tiger)
• Geneious is now only available in one package for Mac OS X. This runs in 64 bit mode by default, but can be changed to run in 32 bit mode.
• Server Databases has been renamed to Shared Databases to avoid confusion with Geneious Server
• Changes to licensing:
  • Geneious Pro/Basic terminology removed
  • Must now enter a license or start trial when starting Geneious for the first time
  • Geneious Pro days no longer occur
• Geneious now collects anonymous usage information (with your permission) to help us make improvements

Patch 6.0.1 (18 October 2012)

• Read Mapper: Faster and produces better results

Bugs fixed:

• Fixed an issue that could cause Geneious to crash frequently on Linux.
• Improved performance of initial document counting in the shared database
• Fixed issue with unformatted sequences being misidentified when starting with ID, FT or SQ
• Fixed crash when trying to add enzymes to list but no enzyme sets in database or inbuilt set
• Fixed crash translating regions from contigs of paired reads
• Improved consensus calling around homopolymer regions in 454 or Ion Torrent data
• Improved behaviour of SAM/BAM files on reads ending before or starting after the area covered by the reference sequence
• Made tracks delete when the last annotation on them is deleted (where that was not already the case)
• Fixed Shared Database compatibility with PostgreSQL 9.
• Primer Design and Testing
  • Better explanations when primer design or testing is unsuccessful
  • Testing now finds primers that bind across the origin of a circular sequence
  • Primer design on alignments now handles gaps more correctly
  • Target region is now respected when designing one primer direction

Patch 6.0.2 (1 November 2012)

• Added fastq export option to export paired reads to parallel files

Bugs fixed:

• Read mapping: Fixed incorrect read mapping results and/or poor performance sometimes with circular reference sequences
• 3D Structure Viewer: Fixed a bug where the selection in the tree was being calculated incorrectly, causing the tree and selections to behave incorrectly
• Fixed bug where extraction of multi-interval annotations from long sequences with many annotations could result in extra annotations
• Made PMID show up correctly on PubMed documents
• Fixed extraction of primers from regions of alignments containing gaps
• Fixed crash when concatenating sequence lists or alignments such that that total number of bases was greater than around 2,000,000,000
• Fixed issue where tree viewer options didn't update when saving document
• Fixed issue where jmol viewer selection misbehaved when a PDB document contains HETATM records prior to the last ATOM record
• Fixed a bug where primer design on alignments would sometimes return primers that were outside the specified product range for some of the aligned sequences
• Fixed a bug where primer testing would annotate matching probes as primers
• Batch rename: fixed a bug where the count and dup keywords weren't working when the new name only consisted of the keyword
• Fixed a bug where test with saved primers would occasionally crash with very old primer documents
• Fixed a bug where primer design would attempt and fail to run with product sizes smaller than the included region
• Added a warning when the user attempts to run an operation that determines primer characteristics, where [dntp] > [divalent salt]. This is currently not supported by primer3
• Fixed crash in the parent-descendant viewer

Patch 6.0.3 (6 November 2012)

• Corrected initial release date

Patch 6.0.4 (28 November 2012)

• Sequence Viewer: Fixed hang working with annotation types in tracks that contain '_' or '.' in their type name
• Sequence Viewer: Fixed crash in rare situations when clicking on annotations in contigs
• Sequence Viewer: Fixed crash and/or loss of newly added annotations on consensus sometimes when saving contigs
• Sequence Viewer: Fixed poor performance/hangs viewing large contigs with non-trim annotations on the reads
• Sequence Viewer: Fixed statistics that are too small to read sometimes
• Reference assembly: Fixed crash and/or incorrect results when choosing to map paired reads to all matching locations.
• Reference assembly: Fixed poor sensitivity mapping to genomes of several hundred MB (larger genome sizes (e.g. human genomes) were fine). The increased sensitivity will also slightly improve small genome results.
• Reference assembly: Fixed poor sensitivity mapping reads spanning the origin of circular reference sequences
• Reference assembly/Find Annotations: Fixed crashes when running out of memory.
• Variant Finder: Fixed crash when there is an insertion variant in a repetitive region at the start of the reference sequence
• Contigs: Fixed crash when creating contigs with a single reference sequence exceeding 1.8GB
• Contigs: Fixed out of memory errors and poor performance when working with lots of contigs
• Contigs: Fixed crash when deleting the ends of circular contigs.
• Fixed crash when using consensus 'Ignore Gaps' setting combined with 'Assign Quality: Highest'
• Fixed crash in MUSCLE alignment when MUSCLE runs out of memory but still returns results
• Streamlined selection in 3D Structure viewer
• Fixed crashes when downloading Whole Genome Shotgun records from NCBI
• Fixed hangs associated with the use of the feature finder
• Fixed bug stopping Geneious from being able to change its max memory on Windows sometimes
• Fixed hang when extracting multiple large regions from a sequence list or contig
• Stopped errors from custom BLAST from being suppressed when the entire BLAST failed
• Fixed Gene documents having their dates one month in the future from where they should be
• Stopped Vector NTI database import from failing completely when a document's parents unexpectedly have length zero
• Fixed multiple dialogs being popped up when queued Sassafras license is checked out but user does not confirm
• Stopped NCBI Gene database downloading documents multiple times when there is a connection error with NCBI
• Added warning when large NCBI BLAST fails due to being too computationally intensive
• Fixed translation in all 6 frames from using frame one only
• Stopped stop codon from being included when extracting translation from sequence viewer

Patch 6.0.5 (12 December 2012)

• Fixed crash sometimes when doing a COGS search
• Fixed a crash that would occur when downloading results of Geneious Server jobs after resuming
• Fixed crash sometimes when creating contigs or sequence lists. Most often when saving unused reads during assembly.
• Fixed crash sometimes when iteratively mapping pre-assembled contigs to a reference.
• Fixed annotations that should be hidden showing up when using 'Find Annotations' or 'Transfer Annotations' and crash when working with them.
• Fixed de novo assembly crash while analyzing reads
• Fixed a crash that would occur when batch renaming a mixture of documents with and without document fields (such as imported BAM files).
• Fixed sequences in alignments getting replaced with contents of other sequences when sequences were deleted or reordered in the sequence list the alignment was built from
• Stopped geneious reporting "hangs" when a dialog is shown for a long time as Geneious starts up
• Fixed crash when extracting duplicate regions from sequence viewer
• Fixed crash downloading some Whole Genome Shotgun sequences from NCBI
• Improved progress when downloading some Whole Genome Shotgun sequences from NCBI
• Improved speed of downloading full NCBI Gene documents
• Stopped crash during import of SAM/BAM files with read groups of expected template length 0
• Improved calculation of expected template length when not given in SAM/BAM file

Patch 6.0.6 (13 February 2013)

• Fixed editing of multiple annotations adding properties present only on one annotation to all the other annotations
• Fixed crash and/or incorrect results in rare cases when mapping reads to a reference sequence with iterative fine tuning
• Fixed crash in rare cases when mapping reads to a circular reference sequence shorter than the read being mapped
• Fixed SAM import issues when some sequences not present, or when using "Use sequences in the selected folder
• Fixed deletion of BLAST databases
• Fixed crash when downloading some SNP results (including in searches of root NCBI folder)
• Fixed issue where BLAST could download wrong results when there were multiple hits against same database sequence

Version 5.6 (27 March 2012)

Parent-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)
• Shared Database: Improved performance

Bugs fixed:

• Reduced memory usage on long-lived databases by storing preferences more efficiently

Additional Notes:

• Existing Shared Databases require an updated schema that will make them incompatible with versions prior to 5.6.0.

Patch 5.6.1 (11 April 2012)

Features 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 shared 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 shared Database to not be available in the primer chooser
• Marking a document read in a shared Database no longer completely re-indexes it

Patch 5.6.2 (23 April 2012)

Features

• 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 shared Database using a number field
• Fixed an issue with Sassafras licenses not working

Patch 5.6.3 (15 May 2012)

Bugs fixed:

• Fixed crash importing or copying some documents into the "Searches" folder or sub-folder
• Fixed crash when viewing some circular sequences
• Fixed crash when saving some sequences from the sequence viewer
• Fixed crash when importing some fasta files
• Fixed crash when mapping reads longer than the circular reference sequence
• Fixed crash when importing files from GenomeQuest
• Fixed annotation type drop down being filled with partial type names after entering a custom type
• Fixed hang when viewing big contigs with annotations on the consensus sequence
• Fixed hang when editing big contigs
• Fixed incompatibility with Microsoft SQL Server
• Fixed annotations going missing in some situations when adding annotations to an alignment/contig which references sequences in a sequence list
• Fixed 'compare annotations' not working correctly with multiple contigs selected
• Made changing restriction site annotations on a sequence not require deactivating active parent links or propagating changes to actively linked descendant documents

Patch 5.6.4 (13 June 2012)

Bugs fixed:

• Sequence Viewer: Fixed the wrong region being selected by a mouse click when rendering is slow
• Sequence Viewer: Fixed crash when clicking the mouse sometimes
• Sequence Viewer: Fixed crash when running an 'Annotate & Predict' operation when "Show annotations" was off
• Sequence Viewer: Fixed crash sometimes when saving tracks
• Sequence Viewer: Fixed crash sometimes when viewing circular sequences
• Reference Assembly: Fixed annotations going missing from reference sequence when fine tuning big contigs
• Reference Assembly: Fixed reads being incorrectly aligned and/or assembler crashing when mapping gappy reads when some of them have trim annotations
• Tree View: Fixed crash when two sequences in a tree have the same name
• Annotation tracks are now preserved when running a BP Reaction
• Fixed potential hang on startup or shutdown when checking license
• Improved support for importing DNAstar, genbank and GFF files
• Fixed crash in custom BLAST when binning sequences into hits and no hits
• Batch rename - now appends the correct parent document name when batch renaming sequences in multiple lists or alignments.

Patch 5.6.5 (26 July 2012)

Bugs fixed:

• Reference Assembly: Fixed crash or mis-assembly of reads mapped to circular sequences that are longer than the reference sequence
• Fasta Importer: Fixed an issue importing flat file with over Integer.MAX_VALUE characters
• BAM exporter: Improved the memory usage when exporting .bai
• Fixed an issue where Insert into Vector was creating the wrong number of intervals on a Multiple Cloning Site annotation.
• Fasta Importer: Improved issue where the importer naming sequences incorrectly when the option to rename identical sequences was on
• SAM importer: Fixed an issue where it was still giving wrong expected distance in some cases
• Fixed an issue where concurrent licenses were sometimes going missing on MacOS X Lion
• Primer Testing: Fixed a crash in characteristics for selection
• BAM importer: Improved memory/disk usage issues in using the Picard libraries
• Circular reference assembler: Fixed an issue when assembling reads more than twice the length of the circular reference
• Annotations table: Fixed 2 occasional crashes
• Shared Database: Fixed an issue where super-admin permissions weren't being realized

Patch 5.6.6 (15 October 2012)

Bugs fixed:

• Fixed issue where consensus tree builder was producing incorrect trees
• Fixed issue where reverse complementing consensus sequences would crash
• Fixed issue where SAM/BAM exporter was recording gapped lengths of sequences in the LN field
• Fixed issue where low complexity filter was ignored in BLASTs sometimes
• Fixed issues where BLAST results did not always include the best hits
• Fixed an issue where the Shared Database could become slower than expected on large MySQL databases
• Fixed an issue where primer documents stored in a Shared Database would show up multiple times
• Fixed ligate operation not respecting reordering of fragements when re-running due to changes in parent document
• Fixed issue introduced recently by NCBI where protein searches would sometimes crash
• Fixed issue where Geneious-style floating license was not always visible to all users once registered

Version 5.5 (30 August 2011)

Sequence 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)
• Fixed an issue which caused adding of documents to a shared Database to be significantly slower in v5.4

Patch 5.5.1 (19 September 2011)

New features:

• Annotations table: Added new columns with the minimum and maximum values in original sequence coordinatesPro-only
• BLAST query and hit sequences have description Pro-only

Bugs fixed:

• Fixed a bug where Batch Rename would fail to rename large sequence lists.
• Greatly improved speed of back up operation when doing full archive backup (no longer uses compression)
• Fixed custom fields being lost when exporting documents in Geneious format and importing them on another machine
• Fixed so that if you unselect the document while an 'annotate & predict' operation is running you can still get the results
• Fixed some fields not getting indexed for searching on big documents
• Fixed out of memory errors when indexing big documents
• Bug fixes in Sequence/Contig Viewer
  • Fixed crashes and hangs caused when trying to view too many tracks to fit in memory
  • Fixed tracks crashing or behaving wrongly after reordering sequences
  • Fixed track names being rendered too close or overlapping with the sequence name
  • Fixed crash when viewing sequence lists containing tracks after some sequences have been deleted from the list
  • Fixed crash when saving some contigs after seeing a conflicting changes message
  • Fixed 'Annotations are arranged more efficiently on genomes' not working on circular genomes
  • Changed units in sequence viewer from Mb to Mbp
  • Fixed annotations in tracks on consensus sequence appearing in the wrong location when 'hide gaps in reference sequence' is on
• Bug fixes/improvements in UCSC annotation track downloads Pro-only
  • Warning if chromosomes are wrong length
  • Nice names for genomes
  • Better sorting for genomes/chromosomes
  • File size does not stop displaying when you change chromosomes
  • Stop displaying tracks that cannot be accessed by HTTP
  • Fix issue where annotations could appear on the wrong chromosomes
  • Allow annotation of sequences regardless of what documents they're grouped into (eg 1 standalone sequence and 2 sequence lists)
  • Fixed horrible performance when running UCSC again without having saved the changes produced from an earlier run
• Improved memory efficiency of BED importer so you can import a densely annotated genome (eg SNP files from UCSC) in a small amount of RAM
• Bug fixes/improvements in SAM/BAM im/exporter
  • Fixed issue finding reference sequences when importing SAM/BAM files with no header
  • Fixed crash when exporting sequence with unreasonably high quality to SAM/BAM format
  • Fixed crash importing with a reference with quality that has gaps introduced
  • Fixed behaviour when importing or exporting contigs where one or more reads start after the end of the reference
  • Fixed crash when file consists entirely of pairs without their mate
• Bug fixes/improvements in extraction/reverse complementing/translating in sequence viewer Pro-only
  • Changed behaviour of extraction of whole sequences from alignment to create new sequences rather than going to existing references
  • Fixed crash when extracting annotation with two identical intervals on same sequence
  • Made options remember preferences on appending "extraction" to names, extracting to alignment vs sequence, extracting selected vs entire sequences
  • If you extract a whole circular sequence from an alignment the result is now circular
• Fixed bug where Jmol viewer did not restore state first time showing molecule after save
• Fixed crash in ACE importer when bases are invalid
• Fixed GenBank importer not offering to create sequence list
• Fixed bug where Geneious thought you could run annotation generators on unaligned sequences when the sequence viewer wasn't loaded
• Fixed assembly crash when assembling existing contigs containing trim annotations covering gapped regions
• Annotations table: annotations that start or end at the origin of a circular sequence now show min/max values of the sequence length rather than 0Pro-only
• Annotations table: now displays annotations from consensus sequence tracksPro-only
• Annotations table: now remembers widths of resized columnsPro-only
• Annotations table: sorts decimal and scientific format numbers correctlyPro-only
• Fixed issue where the extraction of an annotation with overlapping intervals would end up with extra intervals
• Made fasta and fastq importer replace preformance-killing names with better ones

Patch 5.5.2 (26 September 2011)

Bugs fixed:

• Sequence viewer: Fixed tracks and annotation types in tracks sometimes not respecting the on/off state of the checkbox in the controls.
• Sequence viewer: Fixed editing colors of annotation types in tracks not being persistent
• Sequence viewer: Annotation types within tracks and the mini-map are now alphabetically sorted instead of random
• Sequence viewer: Fixed the left/right annotation navigation arrows not being enabled when they should be
• Sequence viewer: Fixed bug when filtering annotations in tracks the mini-map wasn't updated to reflect the filter
• Sequence viewer: Fixed hang loading large sequence lists
• SNP finding: Fixed bug introduced in 5.5.1 where annotations would be offset from where they should be
• Assembly: Fixed trim annotations getting lost during assembly sometimes
• Improved error dialog when a bug in a document causes the search indexer to crash every time Geneious starts. It now tells you how to prevent it from happening in future

Patch 5.5.3 (10 October 2011)

Bugs fixed:

• Assembly: Fixed crash sometimes when generating assembly report
• Assembly: Fixed crash sometimes when assembling gappy reads to a circular reference sequence
• Assembly: Fixed 'Map multiple best matches' mapping reads with gaps to the same location multiple times
• Alignment/Contig Viewer: Fixed 'Hide gaps in reference sequence' discarding annotations covering gapped regions in the reference sequence
• Alignment/Contig Viewer: Fixed crash when saving changes made to some alignments
• Contig Viewer: Fixed changes getting lost in some situations when saving after editing the reference sequence in a big contig
• Contig Viewer: Fixed hang sometimes when selecting on big contig documents
• Sequence Viewer: fixed crash pressing ctrl-alt-g (go to residue) after selecting a document but before the sequence viewer has finished loading
• Sequence Viewer: Fixed crash sometimes if there isn't enough memory to load a big track on a sequence
• Sequence Viewer: Fixed annotations in tracks getting drawn on top of other sequences in some situations
• Sequence Viewer: Fixed crash when editing some trimmed sequences
• Sequence Viewer: Fixed very slow initialization on sequence lists containing thousands of sequences with tracks on each sequence
• Sequence Viewer: Fixed undo not working correctly when dealing with some types of changes to tracks
• Sequence Viewer: Enabled genome viewer chromosome selector (available when at least one sequence has 100,000 or more bases) on sequence lists with more than 1000 sequences
• Local Database: Fixed failure to save documents sometimes
• SNP finder: Running on multiple contigs at once that referenced the same reference sequence would generate identically named tracks and only the first one would get displayed
• Sequence viewer: Fix bad performamce extracting millions of reads from a sequence list
• Sequence viewer: Fix crash extracting sub-alignment containing sequences of all gaps and the consensus
• Fixed tracks not getting saved sometimes when saving them on contigs/alignments
• Fixed a few crashes in the SAM/BAM importer

Patch 5.5.4 (7 November 2011)

Bugs 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

Patch 5.5.5 (21 November 2011)

Bugs fixed:

• Alignment/Contig Viewer: Fixed crash when saving tracks if a track with the same name is created on a referenced sequence from a different view
• Alignment/Contig Viewer: Fixed crash when saving if you had selected an annotation and shift-clicked in another sequence before saving
• Variation/SNP Finder: Fixed crash when using the "Find Only SNPs" option
• Assembly: Fixed crash when using the 'Minimum overlap identity' setting with a circular reference sequence
• Shared Database: Fixed an issue that would create duplicate folders in the Sources tree.
• Shared Database: Fixed a security issue when using the Microsoft JDBC driver and making use of integrated security rather than the one bundled with Geneious.
• Patched NCBI Genome service to mimic its old behaviour after NCBI released a new Genome database incompatible with Geneious

Patch 5.5.6 (5 December 2011)

Bugs fixed:

• Alignment: Fixed annotations not being reversed and lost references when alignment automatically determines directions
• Primer search: Display a message when search index is being rebuilt instead of just showing an empty table
• Worked around a memory leak bug introduced by MacOS Java 6u29 that was causing crashes and freezes after a recent system update from Apple
• Fix issue on Mac OS where the main window would minimize on startup then be unresponsive (also caused by Java update from Apple)
• Shared Database: Fixed excessive slowness when there are a large number of additional document XML keys in the database
• Shared Database: Fixed modification of database blocking retrievals until it completes
• GFF importer: Fixed crash when sequences in list are not editable

Patch 5.5.7 (12 March 2012)

Bugs fixed:

• Sam/Bam importer was using excessive memory and temporary files importing sam/bam files with lots of reference sequences
• Fix hang that could occur on shutdown
• Shared Database: Fixed incompatibility issues with Microsoft's JDBC driver for SQL Server that were introduced in 5.5.6

Patch 5.5.8 (30 April 2012)

Bugs fixed:

• Fixed random crashes revealed by spurious wakeup bug introduced in Java update from Apple
• Fixed crash in the dotplot revealed by bug in Java update from Apple
• Fixed error message in NCBI services due to large batch size requests

Version 5.4 (29 March 2011)

New features added in Pro version only:

• Support for Multi-site gateway cloning
• BAM format import and export (including BAM index file)
• BED format import and export
• SAM format export
• Set the color of folders and documents in local and shared Databases
• RNA Fold viewer scrolls to selection
• Better results when reference sequence assembling.
• Codon usage statistics added to the Statistics tab in the Sequence and Alignment view
• The direction of sequencing reads can be set before the assembly process using "Set Read Direction" in the Sequence menu
• Improved performance and greatly reduced memory usage when dealing with large numbers of sequences (both stand-alone and in contigs)
• BLAST searches now have the option to return a query-centric alignment document only
• BLAST searches now have the option to bin queries into those with hits and those with none, without the need to download entire hits (faster than a standard search)

New 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)

Patch 5.4.1 (19 April 2011)

New 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 shared Databases on start up
• Fixed crash that occurred when deleting documents while having multiple shared 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
• Fixed bug causing large contigs or sequence lists to occasionally crash
• 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

Patch 5.4.2 (25 April 2011)

Bugs 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
• Fixed a crash in BLAST when running a search on PDB documents

Patch 5.4.3 (12 May 2011)

Bugs 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

Patch 5.4.4 (7 June 2011)

Bugs fixed:

• Sequence Viewer: Fixed crash when attempting to display some documents
• Sequence Viewer: Fixed crash when finding ORFs or restriction sites on some sequences that have trim annotations
• Find Variations/SNPs: When analyzing the effect on CDS, the amino acid/codon changes property could sometimes have additional incorrect codons appended to the correct amino acid/codon changes.
• Find Variations/SNPs: If you turned on "Find SNPs Only" for a contig with a reference sequence, next time you search for variations on a contig without a reference sequence, it would find no results
• Fixed an issue with batch rename failing on certain combinations of documents
• Fixed an issue where running sequence searches from old versions of Geneious would crash Geneious on startup
• Fixed crash when importing sequences which contain invalid nucleotide or amino acid characters
• Sequence Viewer: Fixed crash when using 'Color by Annotation' color scheme
• Assembly: Fixed crash when assembling paired reads to a reference sequence on some data sets
• Fixed bug where Annotation Table would sometimes select a different annotation to the one selected in the Sequence Viewer
• Annotation Table now displays the value of "Sequence" annotation qualifiers, rather than displaying the actual sequence the annotation covers
• Contig Viewer: Fixed crash when saving after deleting all the bases from a sequence
• Fixed incorrect PCR product size given in primer annotation
• Fixed crash when exporting .qual format file without accompanying fasta file
• Fixed crash when creating or extracting from big protein alignments
• Fixed issues where 64-bit windows users cannot activate on 32-bit Windows
• Fixed fastq export producing corrupt files on consensus sequences
• Fixed an issue where Geneious had to be restarted in order to use Trim by Vector or COGS BLAST after set up
• Fixed 'Find in document' keeping every document you use it on in memory

Patch 5.4.5 (30 June 2011)

Bugs 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

Patch 5.4.6 (25 July 2011)

Bugs fixed:

• Fixed crash when creating contigs more than 270 million gapped base pairs long
• Fixed some protein sequence lists converting to nucleotide sequence lists or crashing (likely to occur when sequence searching using bin into 'has hit' vs 'not hit')
• Fixed crash when removing trimmed regions from some sequence lists when the trim annotation was selected prior to trimming
• Fixed case sensitivity in Separate by Barcode
• Fixed a problem with the installer which was causing Geneious to crash after upgrading
• Query centric view is no longer Pro-only
• Fixed agents so they won't download the same documents multiple times
• Fixed a problem which was allowing corrupt BLAST agents to be created, crashing Geneious
• Fixed crash when editing a sequence list that had been used as a BLAST query

Version 5.3 (15 November 2010)

New features added in Pro version only:

• Next-Gen Sequencing:
• • Can split unprocessed 454 paired reads apart based on the presence of a linker in the middle of a sequence using 'Set Paired Reads' from the Sequence menu
  • Can split multiplexing data (e.g. 454 MID sequences) using 'Separate Reads by Barcode' from the Sequence menu
  • Can split Polonator paired reads in half from using 'Set Paired Reads' from the Sequence menu
  • The Geneious reference sequence assembler fine tuning option can be applied to existing contigs without needing to reassemble them
• BLAST:
• • Custom BLAST databases created from sequences in Geneious will now store annotations and return fully annotated hits
  • If Maximum Hits is set to 1 in Sequence Search, all results are downloaded to a single folder instead of creating many sub-folders
  • Custom BLAST can now use multiple CPU cores (advanced option added)
  • Blast hits now have a column in the document table listing the percentage of the query sequence covered by the hit
  • Can view query centric alignments vertically compressed (like the 'Vertically Compress Contig' setting in previous versions)
• Full support for importing GFF 3 format annotations and better options for choosing which sequence(s) to annotate
• Trees can now be printed across multiple pages
• ACE format exporter for assemblies
• GC graph now has "frame plot" option to show GC content in each codon position
• Can resize chromatogram traces by dragging them up/down in the Sequence and Alignment Views
• Individual chromatogram traces (A,C,G and T) can be hidden in the Sequence and Alignment Views
• When viewing vertically compressed contigs/alignments, it shows sequence names even when zoomed out if there is only 1 sequence in the row within the visible region
• In an alignment view if you set a reference sequence then the statistics list the percentage of the reference sequence covered by other sequences in the alignment
• Tree view allows setting of a maximum length for tip labels, truncating longer labels
• Binning parameters can be set for individual folders or documents by turning on "Enable per folder/document binning" in the binning preferences
• Primer trimming now has a "Minimum Match Length" option, allowing better trimming of partial primers binding sites
• Go to next/previous disagreement button now skips over the middle of contiguous disagreements
• Sequence Searches now show up in Operations Table
• When assembler saves unused reads it puts unused paired reads in a separate list from unused unpaired reads
• SNP/Variation finder: Added option to not find variations or only find variations in regions covered by particular annotation types

New features:

• Reduced memory usage when importing big sequences, contigs, and alignments

Bugs fixed:

• Editing the consensus sequence in a contig/alignment doesn't modify the reference sequence now
• Fixed assembly sometimes introducing excessive gaps around regions that don't closely align
• Fixed Maq importer setting incorrect paired read expected distance on some contigs
• Numerous small bug fixes in Operations Table
• Fixed incorrect concatention of mixed quality and non-quality alignments
• Ace importer brings in sections of reads which fall outside the consensus
• Trim By primers matches primers partially off the end of a sequence
• Fixed base numbering on blasts that find hits on the reverse complement
• Fixed unresponsiveness when loading long sequences with many restriction sites into viewers
• Fixed bug introduced into multi-user chat in Geneious 5.1
• Max memory setting is now remembered when upgrading Geneious on Mac OS

Patch 5.3.1 (29 November 2010)

Bugs fixed:

• Fixed slow de novo assembly on gapped reads (bug introduced in 5.3.0)
• Fixed crash when trying to reorder a mixture of chromatograms and non-chromatograms in sequence/alignment view (bug introduced in 5.3.0)
• Fixed crash when saving enzyme sets (bug introduced in 5.3.0)
• Fixed 454 sff importer creating leading trim annotations 1 base longer than they should be
• Vector trimming no longer disables other trimming types when run at the same time
• When extracting a primer from the Annotations table, an Oligo sequence is correctly created
• If the options are wrong in document history there is now a button to display the saved xml
• Convert to oligo now correctly retains notes when run on multiple sequences
• ACE exporter now discards the reference sequence if one is present
• Fixed issues in Custom BLAST caused by sequence names containing underscores
• Editing the interval or calculated characteristics of a primer/probe is now disallowed in the sequence view

New features added in Pro version only:

• SNP/Variation finder: Added option to only find variations in regions covered by particular annotation types
• Coverage finder now merges regions where the coverage between them only slightly exceeds the coverage requirements.

Patch 5.3.3 (13 December 2010)

Bugs fixed:

• Fixed crash when using "File->Save As"
• Fixed crash when using "Find Variations/SNPs" on reference sequences with truncated CDS annotations
• Fixed bug where the Add Annotation dialog was crashing when you tried to add or modify intervals and qualifiers
• Variation/SNP finder: Merging of adjacent variations improved so that annotations are only merged as long as the variation is on the same subset of reads (with a small tolerance for read errors). Previously it would just merge all adjacent variants when the variant frequency was over 80%
• Fixed "Go to base" on big contigs causing hangs or running out of memory
• Fixed crash when assembling contigs to a reference sequence
• When assembling contigs containing paired reads to a reference sequence, for contigs that mapped to the reverse strand of the reference sequence, the paired distances were incorrectly set in the results
• Improved primer trimming to fix those cases where it fails to find some primers with mismatches or finds partial primers in the middle of the sequence when it shouldn't
• Updated the Java tools used to manage PDFs
• Fixed PDF documents imported into Geneious were not having their content indexed for search purposes
• Fixed bug in licensing where Geneious thinks a different user activated your license
• Fixed crash in SAM importer with reads starting with an insertion
• Fixed incorrect import in SAM importer when reads overlap the start of the reference sequence

New features added in Pro version only:

• Sequence/Alignment viewer: Can delete all selected annotations of a particular type

Patch 5.3.4 (20 December 2010)

Bugs 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

Patch 5.3.5 (3 March 2011)

Bugs fixed:

• Fixed crash when using "Find Variations/SNPs" on contigs with trim annotations
• Fixed MySQL 5.5 compatibility issue in Shared 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

Patch 5.3.6 (8 March 2011)

Bugs fixed:

• Fixed a frequent crash that was introduced into the shared Database with v5.3.5

Version 5.1 (16 August 2010)

New features added in Pro version only:

• Primer browser - Used for choosing primers for testing and trimming. Allows sorting of primers and grouping them in to folders
• New batch rename with complex replacements and the ability to rename any field
• realign part of an alignment
• Virtual gel viewer now has labels above columns
• Extract PCR can now extract all PCR products or the product from any two selected primers
• GC content graph
• Fragment viewer and digest operation can now digest by each enzyme separately
• Assembler now uses multiple CPU cores for improved performance on multi-core machines
• Ligate Sequences can now be used to ligate a single linear sequence into a circular sequence
• Quality of bases in the consensus can now be calculated as a sum rather than max (more correct)
• Vector NTI gel archive importer (.ga4)
• Sequence view color schemes can now be completely customized
• Document history is now added for assemblies and sequence searches
• Can now add a sequence to an alignment without actually performing an alignment
• Automatic transfer of annotations to a reference sequence from BLAST hits or aligned sequences
• Can manually transfer annotations in query centric BLAST results to the reference sequence
• Can add annotations to sequences in 3D structure documents without needing to create a copy of the sequence
• Assembler now has a Stop button to get results before assembly finishes
• RNA Fold viewer now highlights selections made in other viewers
• Assembler now has Minimum Overlap and Minimum Overlap Identity options
• New distance matrix viewer for trees - includes display of patristic distances and matrix export
• Extract annotations has option to extract entire sequence when it contains a matching annotation
• High/Low coverage finder now has an option to only annotate coverage in genes/CDS regions and average the coverage over the gene
• Find variations/SNPs can now be run on the selected region only
• Digest Sequences now allows cutting at arbitrary selected positions
• Sequence view statistics panel now shows rough DNA melting point
• Annotations can now be modified by dragging the ends of them in the Sequence View
• Non-highlighted characters in an alignment can now be displayed as dots instead of fading their color
• Improved performance and reduced memory usage in both de novo and reference sequence assemblers
• Can assemble to multiple reference sequences
• Can save/generate consensus sequences directly from assembly instead of or in addition to conitgs
• SNP finder records the position of the SNP relative to the start of the CDS annotation it is in
• New assembler can now add sequences to an assembly and assemble sequences together

New features:

• "Operations" table shows the status of all currently running tasks and a history of recently run tasks
• Back Up button added to the toolbar with a greatly improved back up process
• Can now copy text out of annotation information popups in the Sequence View as well as click web links
• Ctrl+clicking (Mac OS: Command+clicking) on annotations allows selecting of multiple regions in Sequence View
• Nexus exporter has option to export simple form with no meta data (required by some other programs)
• The search index can now be paused by clicking on the indexing status on the bottom left
• Fixed issue where licenses bought in the same batch could think they were the same license

Bugs fixed:

• Several improvements to avoid path length limits on Windows systems
• Identity graph and other statistics now correctly ignore trimmed regions

Patch 5.1.1 (3 September 2010)

New features added in Pro version only:

• Improved de novo assembly algorithm to better handle assembly around repeat regions, particularly with paired reads
• Updated Commercially Available Enzymes from Rebase

Bugs fixed:

• Fixed crash when turning off annotations in the sequence viewer after selecting an annotation
• Fixed crash when using live annotate & predict in sequence viewer
• SFF importer now annotates trimmed regions
• Fixed bugs when changing the data location in the welcome dialog when doing a clean install
• Sequence viewer tooltips are now dismissed when you click on them
• Test with Save Primers - "Search for saved primers that match the selected sequences" now works
• Restore Backup in the File menu now works on folder type backups
• Fixed failure to save changes to a sequence after renaming or moving the folder which contains it
• Upgraded Lucene search indexing library used by Geneious which should fix indexing errors for some users
• Improved performance when indexing after modify lots of documents
• Sequence logo graph now ignores the reference sequence
• Searching in sequence/alignment viewer now wraps around to start of the sequence if no matches are found
• Fixed crash when doing consensus alignment
• Fixed an issue where re-rooting an unrooted consensus tree would cause consensus support values to move to the wrong branch
• Tidied up and fixed various issues with the assembly report
• Fixed crash in dotplot when changing settings while data was being generated
• Improved operations table and fixed several issues
• Fixed excessive memory usage and performance issues when trimming sequences from the assembly options
• Improved performance when reference sequence assembling paired reads.
• Installers now do not require administrative privileges, instead requesting them on demand when a FLEXnet license is activated in an environment where FLEXnet isn't installed
• License activation works with proxies with spaces in their names
• Fixed crash when NCBI search is canceled
• Fixed bug in date setback detection

Patch 5.1.2 (15 September 2010)

New features added in Pro version only:

• Reference sequence assembler can now map reads that expand large introns as long as you increase the maximum gap size setting to an appropriate value
• Improved performance when importing millions of sequences

New 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
• MacOS X 10.4 (Tiger) now supports FLEXnet licenses

Patch 5.1.3 (20 September 2010)

Bugs fixed:

• 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 use of -stable flag in MUSCLE
• Progress window is now displayed immediately when adding a custom blast database

Patch 5.1.4 (30 September 2010)

Bugs 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

Patch 5.1.5 (14 October 2010)

Bugs 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 Shared Database
• Fixed occasional crash in RNA Fold viewer

Patch 5.1.6 (19 October 2010)

Bugs 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

Patch 5.1.7 (3 November 2010)

Bugs 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

Version 5.0 (19 April 2010)

New features added in Pro version only:

• Paired end read support - For sequence assembly and contig viewer
• Improved performance and greatly reduced memory usage on big contigs - Can view contigs of 10 million short sequences in 1GB of memory
• Split view - Open documents in multiple views and zoom levels
• Deleted items folder - Restore deleted documents (like Recycle Bin or Trash)
• Document history - Changes to documents are now recorded for later reference
• SNP/Variation finder for contigs and alignments
• Assembly maximum mismatches and maximum gaps settings are now percentages proportional to the sequence or overlap length instead of absolute values
• Virtual gel viewer
• RNA and Primer secondary structure prediction and visualization (uses RNAfold)
• Import and view gel image files
• MAQ alignment format importer
• CAF assembly format importer
• SAM format importer
• FastQ format exporter
• Qual format exporter
• Can sort sequences in an alignment by the bases or residues at a particular position
• Option to specify the minimum confidence (ie. quality) for a call to be made in the consensus sequence
• When a consensus sequence is extracted or generated it will retain calculated quality scores
• High/Low Coverage finder for contigs and alignments
• Non-cutting enzymes are now added to the "Restriction Sites" table when "Find Restriction Sites" is used
• Added shared Database administration interface
• Export images to EPS format
• Basic microsatellite data support (includes .fsa format import and viewer)
• View settings in the sequence view can be saved as preset profiles
• Dotplot now synchronizes its selection with the sequence view
• Keyword filtering in the "Annotations" table view
• Can now add annotations to the consensus sequence in an alignment
• Find in translation for nucleotide sequences in the Sequence View
• Find duplicates can now find duplicates in alignments and sequence lists
• Batch rename now works on alignment and sequence lists
• Concatenate now works on sequence lists

New 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

Patch 5.0.4 (14 July 2010)

Bugs 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
• Fixed an issue where a small number of documents are hidden when initially viewing a folder if that folder contains more than 250 documents
• Addressed issues with large option windows on low resolution screens
• Notes can now be shown on tips in the tree view again

Patch 5.0.3 (8 June 2010)

New 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

Patch 5.0.2 (17 May 2010)

New features:

• Reference sequence assembly now makes use of multiple CPUs. And de novo assembly makes better use of multiple CPUs

Bugs fixed:

• Fixed generate consensus sequence operation in the tools menu putting annotations on the consensus sequence in the wrong place in the generated consensus sequence
• Manually created trim annotations directly adjacent to other leading/trailing trim annotations are now recognized as trim annotations
• Fixed bug where if you trim in the assembly options and are using a reference sequence, the reference sequence gets included twice in the contig
• Fixed crash generating consensus sequence when using the ignore gaps setting
• Fixed sorting sequences in the sequence/alignment crashing sometimes after deleting sequences
• Fixed crash when assembling from a mixture of paired and unpaired sequences
• Fixed crash when reverse complementing some contigs
• Sequence logo graph now ignores regions covered by trim annotations
• Fixed custom assembly options not remembering your preferred settings for next time you do an assembly
• Fixed Geneious crashing on startup sometimes
• Turned off per-document settings in the sequence view by default (can be changed under Appearance & Behaviour tab in preferences)
• Annotations on the consensus sequence were put in the wrong location when "Hide gaps in reference sequence" was on
• Fixed contig viewer bug where consensus and reference sequence were sometimes not rendered when using the paired distance color scheme
• Fixed contig viewer where differences weren't highlighted when using some color schemes or when something was selected
• Fixed reference assembly bug causing some reads to be incorrectly aligned to the reference sequence or occasionally crashing.
• Translation alignment works on local alignment
• Trial activation fixed for 32-bit Linux
• Updated the Sample Plasmids from NEB
• Fragment length column added to enzymes table
• Artemis importer now imports "sequence only" format
• Fixed some crashes in the SAM importer
• Geneious format export now preserves additional data such as document history and per-document settings.
• Viewers now display documents in the same order as the document table
• Consensus sequence now always ignores end gaps on a "free end gap" alignments (ignore end gaps option removed from consensus)
• Shift+Backspace now permanently erases a document/folder on Mac OS

Other:

• Per-document settings turned off by default in Sequence/Alignment View

Patch 5.0.1 (29 April 2010)

New features:

• FastQ importer can now import directly from compressed .fastq.gz files

Bugs fixed:

• Fixed Paired-read de novo assembly not fully using paired-read information
• Fixed "restore defaults" button in assembly options not restoring correct defaults
• Fixed printing circular sequence views
• Fixed crash when using shared Database
• Fixed sorting sequences in the sequence/alignment viewer not working or crashing
• Fixed sequence viewer hanging viewing long reference sequence contigs with under a thousand sequences with quality
• Fixed crash generating consensus sequences in alignments/contigs which have columns of all gaps
• Fixed bugs in SAM importer
• Fixed crash when using similarity color scheme on contigs with trim annotations
• Fixed occasional crash when starting to build an alignment
• Fixed crash when vector trimming
• Fixed crash doing restriction analysis
• Fixed missing task buttons at top of primer design options
• Fixed CAF importer bugs
• Stopped Geneious trying continuously to import sample documents when something goes wrong.
• Fixed failure to import some nexus documents.
• Stopped separate windows viewing the same document from synchronizing their selections unless you turn on a split view
• Fixed sequence/alignment viewer crash when clicking "find previous" in the find window
• Fixed MAQ importer incorrectly importing quality values
• Find Motif now strips invalid characters from the motif to find
• Batch export now warns if there are documents with the same name instead of silently overwriting documents with the same name
• Various document history bug fixes and improvements
• Fixed collaboration crash when sharing two or more folders with the same name
• Fixed crash importing some files containing 10,000 or more sequences
• Fixed bugs to do with annotations on the consensus sequence of an alignment

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 Shared 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 shared 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 shared 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 shared 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
• Shared 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
• Shared 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.
• Shared 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 shared Database plugin relating to referenced documents
• The shared 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 shared Database plugin
• Fixed some memory leaks

Patch 3.5.2 (1 November 2007)

Bugs fixed:

• Various crashes in the shared Database plugin
• Find in annotations on a sequence crash

Patch 3.5.1 (29 October 2007)

Bugs fixed:

• Temporarily hid shared 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:

• MEGA exporter works now

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