MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method |
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Authors: | Changiz Eslahchi Mahnaz Habibi Reza Hassanzadeh Ehsan Mottaghi |
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Institution: | (1) Faculty of Mathematics, Shahid Beheshti University, G.C. Tehran, Iran;(2) School of Computer Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran, Iran |
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Abstract: | Background A phylogenetic network is a generalization of phylogenetic trees that allows the representation of conflicting signals or
alternative evolutionary histories in a single diagram. There are several methods for constructing these networks. Some of
these methods are based on distances among taxa. In practice, the methods which are based on distance perform faster in comparison
with other methods. The Neighbor-Net (N-Net) is a distance-based method. The N-Net produces a circular ordering from a distance
matrix, then constructs a collection of weighted splits using circular ordering. The SplitsTree which is a program using these
weighted splits makes a phylogenetic network. In general, finding an optimal circular ordering is an NP-hard problem. The
N-Net is a heuristic algorithm to find the optimal circular ordering which is based on neighbor-joining algorithm. |
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