Search Mac Software Downloads
|
EDITOR NOTES
This is a beta release. A link for the last stable release is in Related Links below.
DESCRIPTION
Geneious... 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 4.7.1:
  • 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
REQUIREMENTS
  • Mac OS X 10.4 or later
  • Java 1.5 or later.
RELATED LINKS
    Last stable release, v.4.6.5, available here.


SCREENSHOT

Developer:Biomatters Ltd.
Downloads:10,935
  - Version d/l:107
Education:Science
License:Free
Date:29 Jun 2009
Platform:PPC/Intel
OTHER PEOPLE SUGGEST
Suggest something else:
Geneious User Reviews (1 post)Write A Review
sort: smiles | time
Aug 22 2006
*****

MIKENZ  For a long time scientists who generate or analyse DNA sequences have been using multiple pieces of software to: 1) view chromatographs, 2) trim sequences 3) Blast data 4) align sequences 5) build phylogenetic trees. Chopping and changing between different file formats and at times different operating systems (Mac, PC, Unix/Linux) has been a frustrating and time-consuming exercise. Current and future releases of Geneious (www.geneious.com) offer a solution to (most) of these frustrations. The software logo “research in a flash” accurately describe the potential of Geneious – only months after its release it has become the “Swiss army knife” of bioinformatics software.

The user interface of Geneious is both attractive and intuitive. While the software has some “bell and whistles” for more complex tasks one of its key attributes is a simple user interface. Earlier this year I used the Beta-release in some undergraduate teaching labs – with great success. Students did a Genbank search, downloaded files, did an alignment and built a phylogenetic tree (with bootstrapping) all in the blink of an eye. If you are looking for a piece of bioinformatics software for teaching purposes look no further than Geneious.

With the integration of sequence chromatograph viewing and editing of DNA sequences/alignments (new in version 2) Geneious is now firmly embedded in my research practices. As is the case with any new software there are a few features that don’t work quite as well as you might like – but the good news is that if you write to them they will likely fix it up asap. My request to provide a variety of nucleotide colour schemes was implemented within 2 weeks. Moreover, the software is structured in such a way that “new” plugins can be written and incorporated with relative ease.

The Geneious team has made available a freeware version and a pro version that (for a price) allows you to access more functionality. Based on the hours of time this program has saved me already I would not even blink at the academic price tag of $133 (USD) – or cheaper for students.

The software almost has too many features to comment on in any one review (e.g. “agents” and collaboration modes) - the best advice I can give is to download it, do the tutorial and test drive it on a bioinformatics task that you regularly conduct – it won’t disappoint.

Cheers,  
(Version 2.0.4)

praisebury
0
[ Reply ]