Keane, Thomas M. and Naughton, Thomas J. and McInerney, James O. (2007) MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Research, 35 (Web Server Issue). W33-W37. ISSN 0305-1048

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Abstract

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.

Item Type:	Article
Keywords:	MultiPhyl webserver; Bioinformatics; Biology; Genomic data; Phylogenetic analysis; Distributed computing.
Academic Unit:	Faculty of Science and Engineering > Biology
Item ID:	1304
Identification Number:	https://doi.org/10.1093/nar/gkm359
Depositing User:	Dr. James McInerney
Date Deposited:	16 Mar 2009 14:25
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
Refereed:	Yes
URI:	Publisher
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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