“School of Biological”
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Paper IPM / Biological / 14425  


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 ââgenerate â1000 âsets âof âsequences âof âsize at most 30 under biological âpresumptions,â âand âfor âeach âof âthemâ we âobtain aâ âset âof âtriplets âusing âMaximum 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 6â, both methods work nearly the same in time and level of the resulting network. For the networks with level greater than 6â, âthe runtime of Simplistic is very highâ âand in most cases after one hourâ, âSIMPLISTIC does not give any outputâ. âBut the RPNCH runtime for all these cases is at most 4 minutes and the resulting network contains at most 19 reticulation nodesâ. Moreover for complex networks with high levelsâ, âthe Simplistic runtime increased exponentiallyâ. âBut in all cases RPNCH output a network in an appropriate timeâ.
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