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TPMS: a set of utilities for querying collections of gene trees

Thomas Bigot, Vincent Daubin, Florent Lassalle and Guy Perrière*

Author Affiliations

Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard – Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France

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BMC Bioinformatics 2013, 14:109  doi:10.1186/1471-2105-14-109

Published: 27 March 2013

Abstract

Background

The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible.

Results

In this paper, we present TPMS (Tree Pattern-Matching Suite), a set of programs for handling and retrieving gene trees according to different criteria. The programs from the suite include utilities for tree collection building, specific tree-pattern search strategies and tree rooting. Use of TPMS is illustrated through three examples: systematic search for incongruencies in a large tree collection, a short study on the Coelomata/Ecdysozoa controversy and an evaluation of the level of support for a recently published Mammal phylogeny.

Conclusion

TPMS is a powerful suite allowing to quickly retrieve sets of trees matching complex patterns in large collection or to root trees using more rigorous approaches than the classical midpoint method. As it is made of a set of command-line programs, it can be easily integrated in any sequence analysis pipeline for an automated use.