Kumar Sudhir, Tamura Koichiro, Nei Masatoshi
Life Sciences A-351, The Biodesign Institute, Tempe, AZ 85287-4501, USA.
Brief Bioinform. 2004 Jun;5(2):150-63. doi: 10.1093/bib/5.2.150.
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
比较DNA和蛋白质序列分析以分子进化和群体遗传学为坚实的理论基础，在重建物种和多基因家族的进化史、估计分子进化速率以及推断塑造基因和基因组进化的选择力的性质和程度方面发挥着核心作用。由于高通量测序技术以及新颖的统计和计算方法的发展，这些研究的范围如今已大幅扩展。这些方法需要易于使用的计算机程序。其中一项成果就是开发了分子进化遗传学分析（MEGA）软件，其重点在于从进化角度促进对DNA和蛋白质序列变异的探索与分析。MEGA3目前是其第三个主要版本，具备自动和手动序列比对、基于网络的数据库挖掘、系统发育树推断、进化距离估计以及进化假设检验等功能。本文概述了MEGA中用于数据输入的统计方法、计算工具和可视化探索模块，以及可获得的结果。
