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


CONCLUSIONS
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/ and the source code can be downloaded from: http://code.google.com/p/taxomanie/.
Ranwez
Vincent
V
Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E, Bataillon - 34095 Montpellier Cedex 05, France. vincent.ranwez@univ-montp2.fr
Clairon
Nicolas
N
Delsuc
Frédéric
F
Pourali
Saeed
S
Auberval
Nicolas
N
Diser
Sorel
S
Berry
Vincent
V
D003628:Database Management Systems; D030541:Databases, Genetic; D020407:Internet; D010802:Phylogeny; D012984:Software; D014584:User-Computer Interface