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“School of Biological Sciences”

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Paper   IPM / Biological Sciences / 14425
School of Biological Sciences
  Title:   RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function
  Author(s): 
1.  Mohammad Hossein REYHANI
2.  Hadi Poormohammadi
  Status:   To Appear
  Journal: Indian Journal of Science and Technology
  Supported by:  IPM
  Abstract:
Background/Objectives: This paper studies the problem of constructing an optimal rooted phylogenetic network from an arbitrary given set of rooted triplets. Methods/Statistical analysis: We present RPNCH algorithm which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes that contains all the given rooted triplets. We ‎‎generate ‎1000 ‎sets ‎of ‎sequences ‎of ‎size at most 30 under biological ‎presumptions,‎ ‎and ‎for ‎each ‎of ‎them‎ we ‎obtain a‎ ‎set ‎of ‎triplets ‎using ‎Maximum Likelihood criterion. Then we compare the RPNCH results with the SIMPLISTIC results on these data. Findings: SIMPLISTIC is the best algorithm for constructing rooted phylogenetic networks from dense sets of rooted triplets. The results of the comparison between RPNCH and SIMLISTIC on the 1000 simulated data show that when the level of the Simplistic network is at most 6‎, both methods work nearly the same in time and level of the resulting network. For the networks with level greater than 6‎, ‎the runtime of Simplistic is very high‎ ‎and in most cases after one hour‎, ‎SIMPLISTIC does not give any output‎. ‎But the RPNCH runtime for all these cases is at most 4 minutes and the resulting network contains at most 19 reticulation nodes‎. Moreover for complex networks with high levels‎, ‎the Simplistic runtime increased exponentially‎. ‎But in all cases RPNCH output a network in an appropriate time‎.


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