Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

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

Koichiro Tamura1, Joel Dudley, Masatoshi Nei

  • 1Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA.

Molecular Biology and Evolution
|May 10, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Tiny Subsamples and Upsampling Tame Big Data Evolutionary Analysis in Phylogenomics.

bioRxiv : the preprint server for biology·2026
Same author

Universality and diversity of gene expression patterns in response to cold acclimation in Drosophila albomicans.

Genes & genetic systems·2026
Same author

MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems.

Journal of molecular evolution·2025
Same author

Evolutionary sparse learning reveals the shared genetic basis of convergent traits.

Nature communications·2025
Same author

R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework.

ArXiv·2025
Same author

Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits.

bioRxiv : the preprint server for biology·2025
Same journal

The life history of recessive deleterious alleles as seen through the eyes of a honey bee (Apis mellifera).

Molecular biology and evolution·2026
Same journal

Severe bottleneck of ancient Homo populations: Insights from computational modeling and relevant fossil evidence.

Molecular biology and evolution·2026
Same journal

Population Epigenetics: Deciphering DNA Methylation Diversity and its Implications for Health, Disease, and Evolution.

Molecular biology and evolution·2026
Same journal

Genomic signature of repeated transitions to diurnality in spiders.

Molecular biology and evolution·2026
Same journal

Phylogenomic blind spots: The limits of UCE and BUSCO loci in the presence of gene flow.

Molecular biology and evolution·2026
Same journal

seqLens: Optimizing Language Models for Genomic Predictions.

Molecular biology and evolution·2026
See all related articles

The new MEGA 4 software offers enhanced DNA sequence analysis, including automated caption generation for evolutionary models and the novel Maximum Composite Likelihood (MCL) method for distance estimation. This version improves phylogenetic analysis and is accessible on multiple platforms.

Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • MEGA software is widely used for DNA sequence data analysis.
  • Previous versions provided tools for sequence editing, alignment, and phylogenetic inference.
  • There was a need for improved methods for evolutionary distance estimation and clearer reporting of analytical methods.

Purpose of the Study:

  • To announce the release of MEGA version 4, detailing its new features and improvements.
  • To enhance the capabilities for DNA sequence analysis, phylogenetic inference, and evolutionary hypothesis testing.
  • To facilitate a better understanding of analytical assumptions and results through automated caption generation.

Main Methods:

  • MEGA version 4 software release.

Related Experiment Videos

  • Implementation of automated caption generation for analysis descriptions.
  • Inclusion of the Maximum Composite Likelihood (MCL) method for evolutionary distance estimation.
  • Support for multi-threading, multi-user, and cross-platform compatibility (Windows, Linux, Macintosh).

    • Main Results:

    • MEGA 4 provides expanded facilities for DNA sequence editing, database mining, and alignment.
    • A unique feature generates natural language captions for figures, explaining models and methods.
    • The Maximum Composite Likelihood (MCL) method estimates evolutionary distances and substitution patterns efficiently.
    • The software is available as a native Windows application with cross-platform support.

    Conclusions:

    • MEGA 4 offers a significant advancement in molecular evolutionary genetics software.
    • The new features, particularly automated captioning and MCL, enhance usability and analytical rigor.
    • The software continues to be a valuable, free resource for the scientific community.