MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

2011/05/04 by K. Tamura, Koichiro Tamura, Daniel G. Peterson +9 · 39 citations
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #Genetic diversity and population structure #Genomics and Phylogenetic Studies

paper · pdf · doi:10.1093/molbev/msr121

openalex publication_date 2011/05/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/03

Abstract

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.

Citations

• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
• CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
• Evolutionary trees from DNA sequences: A maximum likelihood approach
• A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
• Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

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