MEGA 5 : Molecular Evolutionary Genetics Analysis using Maximum Likelihood , Evolutionary Distance , and Maximum Parsimony Methods

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 MEGA5 (Molecular Evolutionary Genetics Analysis version 5), 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 www.megasoftware.net. 3 The Molecular Evolutionary Genetics Analysis (MEGA) software was developed with the goal of providing a biologist-centric, integrated suite of tools for statistical analyses of DNA and protein sequence data from an evolutionary standpoint. Over the years, it has grown to include tools for sequence alignment, phylogenetic reconstruction and phylogeny visualization, testing an array of evolutionary hypotheses, estimating sequence divergences, web-based acquisition of sequence data, and expert systems to generate natural language descriptions of the analysis methods and data chosen by the user Kumar et al. 2008). With the fifth major release, the collection of analysis tools in MEGA has now broadened to include the Maximum Likelihood (ML) methods for molecular evolutionary analysis. Table 1 contains a summary of all statistical methods and models in MEGA5, with new features marked with an asterisk (*). In the following, we provide a brief description of methodological advancements, along with relevant research results, and technical enhancements in MEGA5. MEGA5 now contains facilities to evaluate the fit of major models of nucleotide and amino acid substitutions, which are frequently desired by researchers (GTR) and five nested models are available, whereas six models with and without empirical frequencies have been programmed for the …

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