tetano
Editor, Senior Moderator
BMC Syst Biol. 2014 Feb 20;8(1):21. [Epub ahead of print]
Quartet-based methods to reconstruct phylogenetic networks.
Yang J, Grunewald S, Xu Y, Wan XF.
Abstract
BACKGROUND:
Phylogenetic networks are employed to visualize evolutionary relationships among a group ofnucleotide sequences, genes or species when reticulate events like hybridization, recombination,reassortant and horizontal gene transfer are believed to be involved. In comparison to traditionaldistance-based methods, quartet-based methods consider more information in the reconstructionprocess and thus have the potential to be more accurate.
RESULTS:
We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS,QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We testedtheir performances and compared them with other popular methods on two simulated nucleotidesequence data sets: one generated from a tree topology and the other from a complicated evolutionaryhistory containing three reticulate events. We further validated these methods to two real data sets: abacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza dataset related to recently emerging H7N9 low pathogenic avian influenza viruses in China.
CONCLUSION:
QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenariosfrom simple branching trees to complicated networks containing many reticulate events. Thesemethods could provide insights into the understanding of complicated biological evolutionaryprocesses such as bacterial taxonomy and reassortant of influenza viruses.
PMID:
24555518
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/24555518
Quartet-based methods to reconstruct phylogenetic networks.
Yang J, Grunewald S, Xu Y, Wan XF.
Abstract
BACKGROUND:
Phylogenetic networks are employed to visualize evolutionary relationships among a group ofnucleotide sequences, genes or species when reticulate events like hybridization, recombination,reassortant and horizontal gene transfer are believed to be involved. In comparison to traditionaldistance-based methods, quartet-based methods consider more information in the reconstructionprocess and thus have the potential to be more accurate.
RESULTS:
We introduce QuartetSuite, which includes a set of new quartet-based methods, namely QuartetS,QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We testedtheir performances and compared them with other popular methods on two simulated nucleotidesequence data sets: one generated from a tree topology and the other from a complicated evolutionaryhistory containing three reticulate events. We further validated these methods to two real data sets: abacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza dataset related to recently emerging H7N9 low pathogenic avian influenza viruses in China.
CONCLUSION:
QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenariosfrom simple branching trees to complicated networks containing many reticulate events. Thesemethods could provide insights into the understanding of complicated biological evolutionaryprocesses such as bacterial taxonomy and reassortant of influenza viruses.
PMID:
24555518
[PubMed - as supplied by publisher]
http://www.ncbi.nlm.nih.gov/pubmed/24555518