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Online Journal of Bioinformatics ©
Volume 14(2):197-206, 2013
Monte Carlo with simulated annealing model for constructing phylogenetic network from nucleotide sequences.
Ashok Kumar Dwivedi1*, Dr. Usha Chouhan2
1Department of Bioinformatics, Mathematics and Computer Applications, Maulana Azad National Institute of Technology, Bhopal, India., 2Department of Mathematics and Bioinformatics, Maulana Azad National Institute of Technology Bhopal, India.
Dwivedi AK, Chouhan U., Monte Carlo with Simulated Annealing Model for Constructing Phylogenetic Network from Nucleotide Sequences, Onl J Bioinform., 14(2):197-206, 2013. A phylogenetic network is used to represent conflicting signals or alternative evolutionary histories in a graph. Phylogenetic networks can be constructed by several methods which are based on various criterions like minimum evolution or maximum likelihood. Some of phylogenetic methods are based on the distances among taxa. In this paper we present an algorithm to find an optimal circular ordering for constructing phylogenetic networks based on the Monte-Carlo with simulated annealing method. We compared the result by applying this algorithm and N-net on same data set. The result shows that this algorithm performs better than N-Net. We find that the circular ordering produced by this algorithm is closer to optimal ordering than N-Net. Furthermore, the networks corresponding to outputs of this algorithm made by Splits Tree are simpler than N-Net.
Keywords: Monte carol, Simulated Annealing, Phylogenetic tree, Phylogenetic Networks, Evolution