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/

FastTree is a program that is downloaded and run locally that generates phylogenetic trees given an alignment MUCH faster than any other available methods, and is scalable to large datasets (e.g. 10,000+ sequences). On a crappy computer, my test showed an alignment of ~750 sequences was able to generate a tree in about 15 seconds.

Analysis of the origins of 2009 swine flu.

Cluster-based analysis of H1N1 origins.

Analysis of the evolution of European swine flu isolates.