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MEGA specifications


Unique identifier OMICS_04236
Alternative names Molecular Evolutionary Genetics Analysis, MEGA X, MEGA-CC
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


No version available


  • person_outline Sudhir Kumar
  • person_outline Koichiro Tamura

Additional information

Publications for Molecular Evolutionary Genetics Analysis

MEGA citations


Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] o for visualization (). Genes on the assembled contigs were predicted with Prokka () using the settings --kingdom Viruses and an e value of 1e−5. Multiple alignments of genes and genomes were made in MEGA7 using the MUSCLE algorithm with default settings (, ). The alignments were manually trimmed, and phylogenetic trees were built using the maximum-likelihood method in MEGA7 with the default setti […]


Smooth muscle like Ca2+ regulation of actin–myosin interaction in adult jellyfish striated muscle

Sci Rep
PMCID: 5958069
PMID: 29773804
DOI: 10.1038/s41598-018-24817-x
call_split See protocol

[…] . Multiple alignments were prepared by the MUSCLE algorithm in Genetyx-Win Ver. 13 (Genetyx) with default settings, and the results were used to construct neighbor-joining phylogenetic trees by using MEGA7 with bootstrap replication set at 1000. […]


AID/APOBEC like cytidine deaminases are ancient innate immune mediators in invertebrates

Nat Commun
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] ltiple sequence alignments were performed using CLUSTALW and optimized manually based on predicted secondary structural features. Phylogenetic and molecular evolutionary analyses were performed using MEGA (version 7). […]


Comparison of the genotypic and phenotypic properties of HIV 1 standard subtype B and subtype B/B′ env molecular clones derived from infections in China

PMCID: 5955974
PMID: 29769530
DOI: 10.1038/s41426-018-0087-0
call_split See protocol

[…] Sequences were aligned using the ClustalW program in MEGA 6.06 software. Phylogenetic analysis was conducted using the neighbor-joining method. Glycosylation sites were predicted with the HIV-1 database online program N-GlycoSite ( […]


Different clusters of Candidatus ‘Methanoperedens nitroreducens’ like archaea as revealed by high throughput sequencing with new primers

Sci Rep
PMCID: 5955947
PMID: 29769540
DOI: 10.1038/s41598-018-24974-z

[…] The protein sequences were first aligned in Clustal X software and then the phylogenetic tree was built using the MEGA software (version 7.0.21) via the neighbour-joining method (1000 replicates). The previously reported M. nitroreducens genomic sequences,,, and reference sequences from diverse environments (rice […]


Novel triple reassortant influenza viruses in pigs, Guangxi, China

PMCID: 5953969
PMID: 29765037
DOI: 10.1038/s41426-018-0088-z

[…] ne segments were aligned and analyzed with the Seqman and Megalign program (DNASTAR, Madison, USA). Phylogenetic trees were generated by applying the method of the Clustal IW alignment algorithm from MEGA 7.0 software (, and bootstrap values of 1000 were used. […]


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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.