Geneious 6.1

v6.0 [12-02-12]

• 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

• 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

• 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

v5.5.3 [10-10-11]

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 server 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)

• 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

• 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)

v5.4.6 [08-02-11]

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 server 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)

• 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

• 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)

v5.4.4 [06-19-11]

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 server 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)

• 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

• 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)

v5.4.2 [04-30-11]

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 server 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)

• 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

• 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)

v5.3.6 [03-27-11]

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

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

• 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

v5.3.5 [03-07-11]

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

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

• 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

v5.3.4 [01-22-11]

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

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

• 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