Journal Article

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

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

in Bioinformatics

Volume 25, issue 1, pages 126-127
Published in print January 2009 | ISSN: 1367-4803
Published online November 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn575

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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 (ML) 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 ML 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@scri.ac.uk

Journal Article.  1182 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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