TPMS: a set of utilities for querying collections of gene trees
File(s)
Published version
Author(s)
Bigot, T
Daubin, V
Lassalle, F
Perriere, G
Type
Journal Article
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.
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.
Date Issued
2013-03-27
Date Acceptance
2013-03-12
Citation
BMC Bioinformatics, 2013, 14 (1)
ISSN
1471-2105
Publisher
BioMed Central
Journal / Book Title
BMC Bioinformatics
Volume
14
Issue
1
Copyright Statement
© 2013 Bigot et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000332199800001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biotechnology & Applied Microbiology
Mathematical & Computational Biology
Biochemistry & Molecular Biology
BIOCHEMICAL RESEARCH METHODS
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
MATHEMATICAL & COMPUTATIONAL BIOLOGY
PHYLOGENETIC ANALYSIS
SEQUENCE DATABASES
COELOMATA
GENOME
CLADE
RECONCILIATION
NUCLEOTIDE
FAMILIES
PATTERN
RNA
Algorithms
Animals
Mammals
Phylogeny
Software
06 Biological Sciences
08 Information And Computing Sciences
01 Mathematical Sciences
Bioinformatics
Publication Status
Published
Article Number
ARTN 109