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EDITOR NOTES

This is a beta release. See Related Links below for the last stable release.

The Download Now link yields the 64-bit version of the beta. For the 32-bit version, see 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.

Download Now
WHAT'S NEW
Version 4.8.0 beta:

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 Server database

REQUIREMENTS
  • Mac OS X 10.4 or later
  • Java 1.5 or later
RELATED LINKS

    Download the 32-bit version of the 4.8.0 beta.

    Download the last stable version (v.4.7.6).

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SCREENSHOT

Developer:Biomatters Ltd.
Downloads:12,693
  - Version d/l:670
Education:Science
License:Free
Date:29 Oct 2009
Platform:PPC/Intel
RATING
*****
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Geneious User Reviews (2 posts)Write A Review
sort: smiles | time
Jul 10 2009
*****

PETE028  Geneious is a superb piece of software for all molecular biologists. I love it. It saved me heaps of time.  
(Version 4.7.1)

praisebury
0
[ Reply ]
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
+1
[ Reply ]