ArticleBMC bioinformatics2013
TPMS: a set of utilities for querying collections of gene trees.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.Genome biology and evolution · 2017Article
- SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.Genome biology and evolution · 2016Article
- Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.Genome biology and evolution · 2013Article
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4 authors.
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Abstract
backgroundThe 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.
resultsIn 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.
conclusionTPMS 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.
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