TPMS is a program suite for bioinformatics. It can manage phylogenetic tree collections, root them, query some peculiar pattern, and detect horizontal transfer.

This suite contains three programs:

tpms_mkdb

create tree collection from tree files, and one species tree

tpms_query

query collections using pattern matching

tpms_computations

(re)root using several methods, detect horizontal transfers

Publication

TPMS: a set of utilities for querying collections of gene trees, 2013
Thomas Bigot, Vincent Daubin, Florent Lassalle and Guy Perrière
BMC Bioinformatics 2013 14:109 DOI: 10.1186/1471-2105-14-109
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-109