Treffer: A perl package and an alignment tool for phylogenetic networks.

Title:
A perl package and an alignment tool for phylogenetic networks.
Authors:
Cardona G; Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain. gabriel.cardona@uib.es, Rosselló F, Valiente G
Source:
BMC bioinformatics [BMC Bioinformatics] 2008 Mar 27; Vol. 9, pp. 175. Date of Electronic Publication: 2008 Mar 27.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:
Evolution, Molecular* , Software*, Gene Expression Profiling/*methods , Proteome/*genetics , Sequence Alignment/*methods , Sequence Analysis, DNA/*methods , Signal Transduction/*genetics, Algorithms ; Base Sequence ; Molecular Sequence Data ; Phylogeny ; Programming Languages
References:
IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):552-69. (PMID: 19875855)
Bioinformatics. 2006 Aug 1;22(15):1921-3. (PMID: 16717070)
IEEE/ACM Trans Comput Biol Bioinform. 2004 Jan-Mar;1(1):13-23. (PMID: 17048405)
Math Biosci. 2008 Feb;211(2):356-70. (PMID: 18177903)
Genome Res. 2002 Oct;12(10):1611-8. (PMID: 12368254)
Mol Biol Evol. 2000 Jun;17(6):875-81. (PMID: 10833193)
Mol Biol Evol. 2001 Jan;18(1):97-9. (PMID: 11141198)
J Bioinform Comput Biol. 2004 Mar;2(1):173-213. (PMID: 15272438)
Syst Biol. 2006 Feb;55(1):46-56. (PMID: 16507523)
Trends Ecol Evol. 2001 Jan 1;16(1):37-45. (PMID: 11146143)
Mol Phylogenet Evol. 2005 Feb;34(2):299-314. (PMID: 15619443)
Substance Nomenclature:
0 (Proteome)
Entry Date(s):
Date Created: 20080329 Date Completed: 20080520 Latest Revision: 20211020
Update Code:
20250114
PubMed Central ID:
PMC2330044
DOI:
10.1186/1471-2105-9-175
PMID:
18371228
Database:
MEDLINE

Weitere Informationen

Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are open-source libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them.
Results: In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself.
Conclusion: The Perl package is available as part of the BioPerl bundle, and can also be downloaded. A web-based application is also available (see availability and requirements). The Perl package includes full documentation of all its features.