PhyloSort (http://phylosort.sourceforge.net) is an open-source user-
friendly Java tool to sort phylogenetic trees by searching for
subtrees that contain a monophyletic group of interest defined by
operational taxonomic units.
Version 1.3 has been released and it is freely available as source
code and binaries (Windows, Mac and UNIX).
The manuscript that describes the implementation of PhyloSort and its
application to estimate the contribution of cyanobacteria to the
nuclear genome of photosynthetic eukaryotes endosymbiotic gene
transfer has been published at BMC Evolutionary Biology (http://