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MEGA5: 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 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.

Pubmed ID: 21546353

Authors

  • Tamura K
  • Peterson D
  • Peterson N
  • Stecher G
  • Nei M
  • Kumar S

Journal

Molecular biology and evolution

Publication Data

October 22, 2011

Associated Grants

  • Agency: NIGMS NIH HHS, Id: R01 GM081066
  • Agency: NHGRI NIH HHS, Id: R01 HG002096

Mesh Terms

  • Algorithms
  • Amino Acid Substitution
  • Bayes Theorem
  • Computational Biology
  • Computer Simulation
  • Data Mining
  • Databases, Genetic
  • Evolution, Molecular
  • Internet
  • Likelihood Functions
  • Models, Genetic
  • Molecular Biology
  • Mutation
  • Phylogeny
  • Sequence Alignment
  • Sequence Analysis, DNA
  • User-Computer Interface