MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0

Koichiro Tamura, Joel Dudley, Masatoshi Nei, Sudhir Kumar

Research output: Contribution to journalArticle

23227 Citations (Scopus)

Abstract

We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, 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 pairs 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 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 version of MEGA is available free of charge at http://www.megasoftware.net.

Original languageEnglish (US)
Pages (from-to)1596-1599
Number of pages4
JournalMolecular Biology and Evolution
Volume24
Issue number8
DOIs
StatePublished - Aug 2007

Fingerprint

genetic analysis
genetic techniques and protocols
Molecular Biology
Software
Sequence Alignment
sequence alignment
software
substitution
Substitution reactions
phylogenetics
Data Mining
Wine
DNA sequences
phylogeny
Composite materials
wines
Language
Nucleotides
nucleotides
methodology

Keywords

  • Cross-platform
  • Genomics
  • Phylogenetics
  • Selection
  • Software

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

MEGA4 : Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. / Tamura, Koichiro; Dudley, Joel; Nei, Masatoshi; Kumar, Sudhir.

In: Molecular Biology and Evolution, Vol. 24, No. 8, 08.2007, p. 1596-1599.

Research output: Contribution to journalArticle

Tamura, Koichiro ; Dudley, Joel ; Nei, Masatoshi ; Kumar, Sudhir. / MEGA4 : Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. In: Molecular Biology and Evolution. 2007 ; Vol. 24, No. 8. pp. 1596-1599.
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