Nucleic Acids Research Advance Access originally published online on June 6, 2007
Nucleic Acids Research 2007 35(Web Server issue):W33-W37; doi:10.1093/nar/gkm359
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W33-W37
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
1Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK, 2Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland and 3Department of Computer Science, National University of Ireland, Maynooth, Co. Kildare, Ireland
*To whom correspondence should be addressed. Tel: +44 (0) 1223 494954; Fax: +44 (0)1223 494919; Email: tkeane{at}cs.nuim.ie
Received January 8, 2007. Revised April 18, 2007. Accepted April 25, 2007.
With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php.
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