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

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      Molecular Biology and Evolution
      Oxford University Press (OUP)

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          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.

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          Author and article information

          Journal
          Molecular Biology and Evolution
          Molecular Biology and Evolution
          Oxford University Press (OUP)
          0737-4038
          1537-1719
          September 20 2011
          October 01 2011
          May 04 2011
          October 01 2011
          : 28
          : 10
          : 2731-2739
          Article
          10.1093/molbev/msr121
          3203626
          21546353
          fa1946c4-5dd6-4ce1-93a9-b128e4d58ae8
          © 2011
          History

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