MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
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DOI：
10.1093/molbev/msm092
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发表时间：
2007-08-01
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;Dudley, Joel;Kumar, Sudhir
我们宣布发布MEGA软件的第四个版本，它扩展了现有的工具，用于编辑来自自动测序仪的DNA序列数据，挖掘Web数据库，进行自动和手动序列比对，分析序列比对以估计进化距离，推断系统发育树和测试进化假设。第4版包括一个独特的设施，以生成标题，写在图例格式，以提供自然语言描述的模型和分析中使用的方法。这一设施旨在促进更好地理解分析中使用的基本假设和产生的结果。另一个新的功能是最大复合似然法（MCL）的方法，估计所有对序列之间的进化距离，同时，与不包括网站之间的变化率和替代模式的异质性之间的谱系。该MCL方法也可用于在不知道系统发育树的情况下估计转换/颠换偏倚和核苷酸替换模式。这个新版本是一个原生的32位Windows应用程序，具有多线程和多用户支持，它也可以在Linux桌面环境（通过Wine兼容层）和Parallels程序下基于Intel的Macintosh计算机上运行。MEGA的当前版本可在http://www.megasoftware.net上免费获得。
We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at http://www.megasoftware.net.