Software

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

Vincent Ranwez¹ , Nicolas Clairon¹ , Frédéric Delsuc¹ , Saeed Pourali^1,2 , Nicolas Auberval¹ , Sorel Diser¹ and Vincent Berry²

¹  Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon – 34095 Montpellier Cedex 05, France

²  Equipe Méthodes et Algorithmes pour la Bioinformatique, LIRMM (UMR 5506 CNRS), Université Montpellier II, Place E Bataillon – 34095 Montpellier, France

author email corresponding author email

BMC Evolutionary Biology 2009, 9:108doi:10.1186/1471-2148-9-108

Published:	18 May 2009

Abstract

Background

Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees.

Results

We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database.

Conclusion

PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/ webcite and the source code can be downloaded from: http://code.google.com/p/taxomanie/ webcite.