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Nucleic Acids Research Advance Access originally published online on October 25, 2007
Nucleic Acids Research 2008 36(Database issue):D491-D496; doi:10.1093/nar/gkm899
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Nucleic Acids Research, 2008, Vol. 36, Database issue D491-D496
© 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-com

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

PhylomeDB: a database for genome-wide collections of gene phylogenies

Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo and Toni Gabaldón*

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler, 13 Valencia 46013, Spain

* To whom correspondence should be addressed. Tel: +34 963289680; Fax: +34 963289701; Email: tgabaldon{at}cipf.es

Received August 14, 2007. Revised October 3, 2007. Accepted October 4, 2007.

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es


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