|MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0|
Tamura K, Dudley J, Nei M, Kumar S
Molecular Biology and Evolution (2007)
Category: bioinformatics ¤ Added: Jul 31, 2007 ¤ Rating: ◊◊
We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from auto-sequencers, mining webdatabases, 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 pair 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 the 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 test version of MEGA is available free of charge at http://www.megasoftware.net.