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Bioinformatics finally gets user friendly

20 April 2006

Bioinformatics finally gets user friendly

If you can use email you can use Geneious 1.0

AUCKLAND: 19 April 2006. Any scientist who uses email can now embark on novel research once considered advanced bioinformatics.

Announcing the launch of Geneious 1.0, which is free to scientists, Daniel Batten, CEO of Biomatters, said, “We are excited about the software and the overwhelmingly enthusiastic response we have had from scientists to making bioinformatics tasks such as sequence alignment, tree building and sequence analysis user friendly.

“The two most common words in user feedback have been ‘long awaited.’”

The beta version was quickly adopted for university courses in Germany and Australia.

Debuting in the top three of Apple’s “Hot Picks,” it also became the second most downloaded piece of software on Apple's Math and Science site.

In helping bioinformatics deliver on its promise Mr Batten said the team led by Dr Alexei Drummond aimed to put advanced computer-based research into the hands of all molecular scientists as a first step towards radically faster and easier research.

“There’s no shortage of clever algorithms. The problem has been that the majority of scientists can’t access them,” Mr Batten said.

“The technology is locked up in bespoke systems, or requires specialist skills, or you have to cut and paste across several applications.

“For example, the workflow of BLASTing sequences, viewing dotplots, conducting multiple alignment, building a phylogenetic tree and comparing annotations against gene similarity meant accessing specialist expertise or withstanding lots of repetitive manual operations. But using Geneious this work can all be done in a few clicks.”

At the University of Veterinary Medicine in Hannover students unanimously voted Geneious number one for ease of use.

“Geneious pulls all key functions into the one package,” Mr Batten said.

“Using open plug-in API technology it also quickly incorporates updates. The system’s phylogenetic tree viewer, for example, represented a lot of academic development but was integrated into Geneious in one day.”

The 1.0 version enables click-and-drag downloads of journals into local libraries, sequence searches on the fly, 3D protein structure viewing and a new way to view gene annotations and similarity at the same time.

Researchers can download Geneious 1.0 free at

Key features of Geneious 1.0

Geneious 1.0 provides an intuitive user interface for searching, sorting and storing biomolecular sequence data and scientific publications, including the following features:

- Phylogenetic reconstruction (NJ with bootstrapping) & tree viewing
- Multiple & pairwise sequence alignment
- Sequence alignment
- Fast dotplots
- Sequence viewing, including sequence annotations from NCBI database from DNA to amino acids and reverse complements
- Export to Endnote, Nexus, Newick, Fasta
- Import trees, sequences, alignments and bibliographies in a variety of formats
- Adding user information and notes to sequences, alignments and trees
- NCBI Blast
- 3D protein structure viewing
- Fast local database searching
- PDF full text searching of publications
- Unlimited undo and redo capability
- It’s free for academic use


Geneious puts core bioinformatics functions within the reach of all molecular biologists and biochemists in an application that is as easy to use as email.
Geneious does sequence alignment, 3D structure visualization, phylogenetic tree building, sequence analysis, publication-search and more; all in a single application.

Biomatters Ltd
Biomatters combines statistical, biological and computational knowledge with user-friendly front-ends to create research platforms that greatly speed up the processes of scientific and medical discovery. In our first two years Biomatters has launched two software packages.


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