Research On Algorithms Of Constructing Phylogenetic Network Based On The Rooted Phylogenetic Trees

Phylogenetic trees and phylogenetic networks are used to illustrate the evolutionary relationship between biologies.Among them,the phylogenetic networks are the general form of the phylogenetic trees.The construction of phylogenetic networks is of guiding significance to the study of species evolution and species modification.Therefore,the construction of phylogenetic networks is one of the important research directions of bioinformatics.This thesis deeply studies the relationship between phylogenetic network and phylogenetic tree and the phylogenetic network construction algorithm based on rooted phylogenetic tree.The main contents of this thesis are as follows:(1)An algorithm for calculating the phylogenetic trees represented by the phylogenetic networks-the toTree algorithm is proposed.The algorithm uses the idea of depth-first traversal(DFS)to calculate the phylogenetic tree represented by the phylogenetic network,which is achieved by reducing some repeated operations to reduce the time complexity of the algorithm.(2)An algorithm for determining whether the phylogenetic network indicates the phylogenetic trees – the toTreeC algorithm is proposed.The toTreeC algorithm detects the tree situations that the phylogenetic network do not indicate the phylogenetic trees.If these conditions do not exist,the toTree algorithm and the equivalent algorithm are combined to determine whether the system occurrence network represents the phylogenetic trees.In this thesis,the toTreeC algorithm is used to evaluate the accuracy of the phylogenetic network construction algorithm.(3)An algorithm of phylogenetic network construction based on root phylogenetic tree-CSFD algorithm is proposed.In this thesis,the current efficient phylogenetic network constructing algorithm-CASS algorithm is improved.On the basis of CASS algorithm,this thesis proposes an improved CASS algorithm-CSFD algorithm,which combines seed-growing algorithm,species frequency and toTreeC algorithm.Experiments show that the CSFD algorithm is superior to the CASS algorithm in resisting data input order,running time and number of redundant clusters.