Geneious 5.3.1 - Sequence analysis software for all molecular biologists. (Free)

Geneiousis research software for biologists, not computer scientists.

Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution! Its ease of use makes bioinformatics accessible to any biologist. It even runs on all major operating systems and is very affordable.

Features include: Sequence alignment, Contig assembly, primers, restriction analysis, BLAST, phylogenetics, automatic publication updates and more.

WHAT'S NEW

Version 5.3.1:

New features

• 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
• Whole Genome Shotgun sequences from NCBI can be imported and downloaded
• 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

REQUIREMENTS

• Mac OS X 10.4 or later
• 64-bit version requires at least 4GB RAM
• Java 1.5 or later

PRICE

Free

DEVELOPER

DOWNLOADS

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