title: Constructing circular phylogenetic networks from weighted quartets using simulated annealing.
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.
authors: Faculty of Mathematics, Shahid Beheshti University, G.C., Tehran, Iran. ch-eslahchi@sbu.ac.ir
authors: Changiz
authors: C
authors: Eslahchi
authors: Reza
authors: R
authors: Hassanzadeh
authors: Ehsan
authors: E
authors: Mottaghi
authors: Mahnaz
authors: M
authors: Habibi
authors: Hamid
authors: H
authors: Pezeshk
authors: Mehdi
authors: M
authors: Sadeghi
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D019143:Evolution, Molecular; D008957:Models, Genetic; D009010:Monte Carlo Method; D010802:Phylogeny