MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
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DOI：
10.1093/molbev/msr121
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发表时间：
2011-10-01
影响因子：
10.7
通讯作者：
Kumar, Sudhir
中科院分区：
文献类型：
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作者：
Tamura, Koichiro;Peterson, Daniel;Kumar, Sudhir
分子序列数据的比较分析对于重建物种的进化历史和推断塑造基因和物种进化的选择力的性质和程度是必不可少的。在这里，我们宣布发布分子进化遗传学分析版本5（MEGA5），这是一个用户友好的软件，用于挖掘在线数据库，构建序列比对和系统发育树，并在基础生物学，生物医学和进化中使用进化生物信息学方法。MEGA 5中最新增加的是一组最大似然（ML）分析，用于推断进化树、选择最佳拟合替换模型（核苷酸或氨基酸）、推断祖先状态和序列（沿着概率）以及逐个位点估计进化速率。在计算机模拟分析中，ML树推理算法在MEGA5中与其他软件包相比，在计算效率和系统发育树估计的准确性，替代参数和站点之间的速率变化方面表现出色。MEGA用户界面现已增强为活动驱动，使初学者和经验丰富的科学家都能更轻松地使用。此版本的MEGA适用于Windows平台，它已被配置为在Mac OS X和Linux桌面上有效使用。可从http://www.megasoftware.net免费获得。
Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.