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Nucleic Acids Research Advance Access originally published online on April 22, 2007
Nucleic Acids Research 2007 35(Web Server issue):W38-W42; doi:10.1093/nar/gkm224
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W38-W42
© 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.

Articles

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

Joaquín Tárraga1,2, Ignacio Medina1, Leonardo Arbiza1, Jaime Huerta-Cepas1,2, Toni Gabaldón1, Joaquín Dopazo1,2 and Hernán Dopazo1,*

1Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF) and 2Functional Genomics Node, INB, CIPF, Valencia 46013, Spain

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

Received January 30, 2007. Revised March 23, 2007. Accepted March 28, 2007.

Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es.


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