Geneious 5.5

Geneious 5.5

User Rating: Fair (0.00/5)

Free for non-commercial use
Biomatters Ltd.|More programs
March 27th, 2012

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50.41 MB|0 downloads

Geneious 5.5 Description

Geneious 5.5 is known as an easy as well as efficient free application from the Geneious software suite - the award-winning DNA and protein sequence analysis software package from Biomatters Limited.

Geneious Basic focuses on three major software requirements among researchers. The first is the ability to import and export any open file formats, making Geneious Basic a perfect file conversion tool. The second is its outstanding user interface for visualization of data sets of any size. The third is Geneious' suitability as a teaching tool. 

  • 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 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 server database to be significantly slower in v5.4
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