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Bioinformatics Advance Access published online on November 4, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn575
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

Iain Milne 1,*, Dominik Lindner 2, Micha Bayer 1, Dirk Husmeier 3, Gráinne McGuire 3, David F. Marshall 1 and Frank Wright 2

1Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK.
2Biomathematics and Statistics Scotland (BioSS), SCRI, Invergowrie, Dundee DD2 5DA, UK.
3Biomathematics and Statistics Scotland (BioSS), JCMB, The King's Buildings, Edinburgh EH9 3JZ, UK.

*To whom correspondence should be addressed. Dr. Iain Milne, E-mail: iain.milne{at}scri.ac.uk


  Abstract

Summary: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian Inference and Maximum Likelihood approaches, in addition to recombination detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from Maximum Likelihood co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes.

Availability: freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.

Contact: iain.milne{at}scri.ac.uk

Associate Editor: Prof. Martin Bishop

Received on August 2, 2008; revised on November 3, 2008; accepted on November 3, 2008

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