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

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.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.Evolutionary biologists now have to deal to an increasing extent with many phylogenetic trees and user-friendly bioinformatic tools are needed for handling large tree collections. Such tools are especially relevant for tasks that are cumbersome to perform manually, such as validating taxon names using a reference taxonomy, providing taxon sampling statistics, or pruning source trees so that they only contain taxa from a taxonomic group of interest. Such questions are crucial in phylogenomics, where phylogenies are mainly obtained by concatenating gene sequences into large molecular datasets (e.g. supermatrix approach) or by combining individual trees inferred separately on each gene (e.g. supertree approach). Several problems addressed here from a tree framework standpoint only take their constitutive taxa into account. Described solutions are thus also suitable for many other kinds of data (e.g. sequence alignments, morphological measures), for which taxonomic representation is essential.Knowing how many different taxa belonging to a particular taxonomic group (e.g. placentals) are represented in a tree collection, determining how many trees contain at least one placental, finding these trees, and pruning them from every taxon except mammals are various tasks that cannot be performed with