PHYML and Shannon Entropy plugins win Geneious Plugin competition
Posted on 24 Oct 2006 10:06
Thanks to everyone who sent in plugins to Biomatters. With over 300 developers who have registered as Biomatters' plugin developers, Geneious is now developing even more rapidly than ever with the world adopting Geneious both as the desktop bioinformatics platform of choice, and now their development framework.
Out of all plugins received, the best ones have been evaluated and we are pleased to announce the winners
1st prize – trip to New Zealand: PHYML from Vincent Lefort and Dr Stephane Guindon Montpellier FRANCE
2nd prize: Dr Joe Parker from Oxford, UK takes 2nd prize with Shannon Entropy Alignment.
2nd prize wins a Free copy of Geneious Pro, plus 2 Geneious Pro licenses to give to your buddies + a Geneious T-Shirt
Congratulations to Vincent and Joe, our first two plugin winners.
Why these plugins are cool
PHYML
This awesomely powerful plugin uses maximum likelihood (ML) calculations to build phylogenetic trees from alignments. Along with Bayesian inference techniques, ML is the best way to build trees; because it uses a statistical modeling method. Users in the field have credited PHYML with being 80 times faster that the industry standard PAUP* at doing ML trees, making ML practical for large data sets. Now that PHYML is available as a plugin to Geneious, it has a great user interface too, making Maximum Likelihood phylogenetics available and useful to everyone in the community.
Shannon Entropy alignments
This great little plugin lets you graphically measure diversity along a sequence. A high entropy score corresponds to a maximally different area of a gene of interest.
Shannon was the biologist who originally developed Shannon entropy to describe species diversity in an ecosystem, and it is now also used to describe nucleotide diversity in a sequence.
How to I get these plugins?
Both these plugins have cleared the bar, and are available from our website. Click the "Download" tab in www.geneious.com on our homepage. These plugins runs straight off Geneious seamlessly like its part of the same application, just double click, install and you have powered up the most powerful desktop bioinformatics tool available to molecular biologists today.