MEGA pipeline

MEGA specifications


Unique identifier OMICS_04236
Alternative names Molecular Evolutionary Genetics Analysis, MEGA5, MEGA2, MEGA3, MEGA4, MEGA6, MEGA7
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 7.0
Stability Stable
Maintained Yes


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  • person_outline Sudhir Kumar <>
  • person_outline Koichiro Tamura <>

Additional information

Publications for Molecular Evolutionary Genetics Analysis

MEGA citations

PMCID: 5952423

[…] sequences and deduced amino acid sequences of individual viral genes were performed by the neighbor-joining algorithm as implemented in clustalw, and the resulting alignments were analyzed using mega7 [6]. recombination analysis was carried out using rdp 4.83 package [7]., to verify the luteovirus sequences are associated with graft-transmissible agents, dormant buds of each of four selected […]

PMCID: 5944068

[…] accession numbers mf503141–mf503148., sequences were edited and assembled using geneious® v.9.1.7 software (biomatters limited, auckland, new zealand) [50]. phylogenetic analysis was conducted using mega7 [51]. sequences were aligned to additional reference sequences retrieved from genbank using the clustal w algorithm. the phylogenetic tree was inferred using the maximum-likelihood method using […]

PMCID: 5919639

[…] amino acid alignment of fatty acid desaturases was performed by clustalx 2.1 program with default setting [40]. a phylogenetic tree was constructed using the neighbor-joining method in mega5 [41]. promoter prediction and cis-acting regulatory element analysis were carried out on the plantcare ( [42]., total rna […]

PMCID: 5904414

[…] were compared with available leptospira sequences representing pathogenic, intermediate, and saprophytic strains. nucleotide alignment was performed in geneious 10.1.2 (64) and exported to mega7 (65). a maximum likelihood tree was prepared with the kimura two-parameter model (k2) using discrete gamma distribution (+g) with invariant sites (+i) and 500 bootstraps. newick trees […]

PMCID: 5901876

[…] trees comparing protein sequences were generated using the molecular evolutionary genetics analysis (mega6) software program [65]. protein sequences were aligned using the muscle program within mega6 [66, 67]. phylogenetic reconstruction was accomplished using the maximum likelihood statistical method, and distances between sequences were determined using 1000 bootstrap replicates., bl […]

MEGA institution(s)
Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia; Institute for Genomics and Evolutionary Medicine, Temple University,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan; Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
MEGA funding source(s)
Supported in part by research grants from National Institutes of Health (HG002096-12) and Japan Society for the Promotion of Science (JSPS) grants-inaid for scientific research (24370033).

MEGA reviews

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Amr Galal

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the tool with windows is working well but not working on linux normally

Erica Souza

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It is a free phylogenetic tool which allow MEGA to reach many users. Although this, it is necessary that users know that MEGA is a blackbox, and you cannot change the software parameters, if you are a beginner in this area you can use the software without doubt it methods, but if you are an advanced user, you should looking for another software.