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Paper   IPM / Biological / 13174
School of Biological Sciences
  Title:   Constructing Circular Phylogenetic Networks From Weighted Quartets Using Simulated Annealing
1.  C. Eslahchi.
2.  R. Hassanzadeh.
3.  E. Mottaghi.
4.  M. Habibi.
5.  H. Pezeshk.
6.  M. Sadeghi.
  Status:   Published
  Journal: Mathematical Biosciences
  No.:  2
  Vol.:  235
  Year:  2012
  Pages:   123-127
  Supported by:  IPM
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.

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