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Similarity Metrics and Their Application in Phylogenetic Analysis

Author: LiZhe
Tutor: ZhouLiQian
School: Xiangtan University
Course: Computational Mathematics
Keywords: similarity measure distance matrix phytogenetic tree
CLC: Q344
Type: Master's thesis
Year: 2013
Downloads: 26
Quote: 0
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Abstract


Phylogenetic analysis is important and widely used in the field of biologicaland medical sciences, and constructing phylogenetic tree is an important task forphylogenetic analysis. we focus on how to construct a phylogenetic tree in thispaper.Phylogenetic trees are usually constructed with the general maximum like-lihood method, the maximum parsimony method and the distance method. Thedistance method is achieved by definition the distance metric between biologicalsequences, and generating a distance. However, most of distance metrics whichused to build phylogenetic trees, do not meet the definition of distance metric inthe mathematical sence, which are called similarity measure by some academics.Inthis paper, we consider the general definition of the similarity measure.First of all, this paper gives a more general definition of similarity measure,then studies its properties and relationship with the distance metric. At the endof this paper, We constructed phylogenetic tree by using the similarity metricand the fact “the greater similarity, the nearer the distance”, and gets a goodphylogenetic trees using the distance matrix, and illustrates the rationality andapplicability of the definition.

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CLC: > Biological Sciences > Genetics > Genetics subdiscipline > Occurrence of genetic ( developmental genetics ),physiological genetics
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