The central task in the research of molecular evolution may be the reconstruction of a phylogenetic tree from sequences of taxa. So, phylogenetic tree is also known as the evolutionary tree, which uses a kind of graph similar to the tree branch to represent the genetic relationship among the organisms and infers the evolutionary history of the species based on the study of biological sequences. The result of phylogenetic analysis is usually expressed in the form of phylogenetic tree. This paper makes estimations on the parameters of the phylogenetic tree by EM algorithm to estimate the optimum length of the branch under parameter model to pave the way for constructing a better phylogenetic tree.
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