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/

A concept for data publication and semantic enhancements proposed by ZooKeys and applied in the milestone paper of Miller et al. (2009) is described. For the first time in systematic zoology, an unique combination of data publication and semantic enhancements is applied within the mainstream process of journal publishing, to demonstrate how: (1) All primary biodiversity data underlying a taxonomic monograph are published as a dataset under a separate DOI within the paper; (2) The occurrence dataset is discoverable and accessible through GBIF data portal (data.gbif.org) simultaneously with the publication; (3) Occurrence dataset is published as a KML file under a distinct DOI to provide an interactive experience in Google Earth; (4) All new taxa (42) are registered at ZooBank during the publication process (mandatory for ZooKeys); (5) All new taxa (42) are provided to Encyclopedia of Life through XML mark up on the day of publication (mandatory for ZooKeys). It is proposed to clearly distinguish between static and dynamic datasets in the way they are published, preserved and cited.