Geneious

Infobox Software
name = Geneious



caption =
developer = Biomatters Ltd.
latest release version = 4.0.2
latest release date = 17 September 2008
latest preview version =
latest preview date =
operating system = Windows, Linux, Mac OS X, Solaris
platform = Java
genre = Bioinformatics
license = commercial (Pro), free for academic use (Basic)
website = http://www.geneious.com

Geneious is a commercial, cross-platform bioinformatics application.

Features

Geneious comes in a basic version that is free for academic use, and a commercial Pro version with added features. Geneious tries to bundle various bioinformatics tools under one hood.

* Sequence alignment and Sequence viewing
* Motif search and open reading frames (ORFs)
* Phylogenetic tree building UPGMA, Neighbour joining with bootstrapping and consensus trees
* Contig assembly and chromatogram editing
* Restriction analysis - find and view restriction cut sites and perform restriction enzyme digests
* PCR Primer design - designing and testing, degenerate primers, mismatches and multiple primer searching
* Protein structure viewer
* Database integration - integrated searching with Genbank, PubMed, BLAST and UniProt
* Collaborate and share data over the internet
* Teach bioinformatics - Create tutorials with direct links to material in Genieous
* Public API to develop free bioinformatics plugin by the community
* Various standard bioinformatics applications such as ClustalW, MrBayes, EMBOSS, Mauve, MUSCLE and PAUP*

Popularity and awards

According to its authors, in May 2007 Geneious had 50,000 users from 30 countries [ [http://www.in-sequence.com/issues/1_18/new_products/139909-1.html Beckman Coulter, Cartesian Gridspeed, GenomeQuest, University of California, Santa Cruz, Biomatters ] ] , and it has gathered attention on GenomeWeb [http://www.genomeweb.com/cgi-bin/texis/scripts-genomeweb/genomeweb-search/search.html?query=geneious&Go.x=0&Go.y=0 GenomeWeb] ] , BioInform, Bio-IT World [http://www.google.com/search?num=100&hl=ensafe=off&q=site%3Abio-itworld.com+%22geneious%22&btnG=Search Bio-IT World] ] and bioinformatics blogs [http://blindscientist.genedrift.org/2007/02/26/hello-world/ BlindScientist blog] ] [ [http://technocrat.net/d/2006/4/20/2665 Technocrat blog] ] . It was also awarded the 2007 World Summit Award in the category e-science [ [http://www.wsa-awards.org.nz/award/2007_winners.html 2007 World Summit Awards] ] , and a 2007 Computerworld Excellence award for innovative use of ICT [ [http://computerworld.co.nz/cwea.nsf/UNID/3DC703C7A4CD0273CC2572DC007B51C1?OpenDocument 2007 Computerworld excellence awards] ] .

Criticism

Geneious is sometimes criticized for trying to be everything to everyone, leading to obscure, not frequently used features and a long startup time (citation needed). It has also been criticized for being commercial, and for not offering unique killer features not available in any of its competitors [ [http://blindscientist.genedrift.org/2007/03/02/geneious-one-year-or-almost-later/ Geneious: one year (or almost) later ] ] .

References

External links

* [http://www.geneious.com/ Geneious Official website]
* [http://www.biomatters.com/ Biomatters website]

[http://evolution.genetics.washington.edu/phylip/software.html List of phylogeny software] , hosted at the University of Washington

Other Software

* [http://www.csc.fi/english/research/sciences/bioscience/programs/ds Discovery Studio]
*Vector NTI
* [http://www.clcbio.com/main CLC Main Workbench]
*UGENE