Who is Who in Phylogenetic Networks

Publication no #2162   Type :   Html | Bib | Both

Created: 2011-12-13 17:58:29     Modified: 2012-04-07 12:35:01

2162 Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012. Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network. Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.         Toggle abstract "In this paper, we present a heuristic algorithm based on the simulated annealing, SAQ-Net, as a method for constructing phylogenetic networks from weighted quartets. Similar to QNet algorithm, SAQ-Net constructs a collection of circular weighted splits of the taxa set. This collection is represented by a split network. In order to show that SAQ-Net performs better than QNet, we apply these algorithm to both the simulated and actual data sets containing salmonella, Bees, Primates and Rubber data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree4 and compare the results. We find that SAQ-Net produces a better circular ordering and phylogenetic networks than QNet in most cases. SAQ-Net has been implemented in Matlab and is available for download at http://bioinf.cs.ipm.ac.ir/softwares/saq.net. © 2011 Elsevier Inc." @Article{EHMHPS2012,       AUTHOR = {Eslahchi, Changiz and Hassanzadeh, Reza and Mottaghi, Ehsan and Habibi, Mahnaz and Pezeshk, Hamid and Sadeghi, Mehdi},       TITLE = {Constructing circular phylogenetic networks from weighted quartets using simulated annealing},       YEAR = {2012},       JOURNAL = {MBIO},       VOLUME = {235},       NUMBER = {2},       PAGES = {123-127},       URL = {http://dx.doi.org/10.1016/j.mbs.2011.11.003},       NOTE = {http://dx.doi.org/10.1016/j.mbs.2011.11.003},       KEYWORDS = {abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network} }