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OJBTM
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