The Study of Calculating Evolutionary Distance

• Main Authors: Yi-yu Hsu, 徐禕佑
• Other Authors: Koun-Tem Sun
• Format: Others
• Language: zh-TW
• Published: 2008
• Online Access: http://ndltd.ncl.edu.tw/handle/03855523662035176002

碩士 === 國立臺南大學 === 數位學習科技學系碩士班 === 96 === In molecular biology, analysis of phylogenetic relationship for evolutionary research is an important issue. The basic structure for calculating evolutionary distance is predicting the mutations between sequences by using approriate models of nucleotide substitution rate. In the past, many researches pointed out distinct evolutionary models under different evolutionary assumptions, such as JC, K2P, K3P, GTR and LogDet etc. However, inappropriate assumptions would underestimate the genetic distance. In oreder to calculate correct evolutionary distance for homogeneity, heterogeneity, stationary, non-stationary, transitional, transversional, synonymous and non-synonymous cases, we propose enchanced two-phase (ETP) method. The method not only adjusts the error in calculation of heterogeneity by TP, but also considers the effect on non-synonymous mutations when nucleotides transfer to amino acids. By downloading the real species sequences from NCBI data base, evolutionary distance calculation and phylogenetic tree analysis for the ETP are verified, and we find that the ETP has better accuracy about 5~20% than other proposed methods. As a result, the ETP has become a useful biotechnology tool in phylogenetic analysis.