MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment - PubMed (original) (raw)
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
Sudhir Kumar et al. Brief Bioinform. 2004 Jun.
Abstract
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
Similar articles
- MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S. Tamura K, et al. Mol Biol Evol. 2007 Aug;24(8):1596-9. doi: 10.1093/molbev/msm092. Epub 2007 May 7. Mol Biol Evol. 2007. PMID: 17488738 - MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. Tamura K, et al. Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4. Mol Biol Evol. 2011. PMID: 21546353 Free PMC article. - MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.
Kumar S, Nei M, Dudley J, Tamura K. Kumar S, et al. Brief Bioinform. 2008 Jul;9(4):299-306. doi: 10.1093/bib/bbn017. Epub 2008 Apr 16. Brief Bioinform. 2008. PMID: 18417537 Free PMC article. - MEGA biocentric software for sequence and phylogenetic analysis: a review.
Sohpal VK, Dey A, Singh A. Sohpal VK, et al. Int J Bioinform Res Appl. 2010;6(3):230-40. doi: 10.1504/IJBRA.2010.034072. Int J Bioinform Res Appl. 2010. PMID: 20615832 Review. - Multiple sequence alignment: in pursuit of homologous DNA positions.
Kumar S, Filipski A. Kumar S, et al. Genome Res. 2007 Feb;17(2):127-35. doi: 10.1101/gr.5232407. Genome Res. 2007. PMID: 17272647 Review.
Cited by
- Exploring pangenomic diversity and CRISPR-Cas evasion potential in jumbo phages: a comparative genomics study.
Magar S, Kolte V, Sharma G, Govindarajan S. Magar S, et al. Microbiol Spectr. 2024 Oct 3;12(10):e0420023. doi: 10.1128/spectrum.04200-23. Epub 2024 Sep 12. Microbiol Spectr. 2024. PMID: 39264185 Free PMC article. - Molecular identification and eco-friendly management of rice brown planthoppers in Bangladesh.
Kar M, Jahan SMH, Rahman MA, Datta SD. Kar M, et al. Heliyon. 2024 Jul 31;10(15):e35514. doi: 10.1016/j.heliyon.2024.e35514. eCollection 2024 Aug 15. Heliyon. 2024. PMID: 39166075 Free PMC article. - Degradation and mechanism analysis of protein macromolecules by functional bacteria in tobacco leaves.
Jiang C, Kong D, Li Y, Sun J, Chen Z, Yang M, Cao S, Yu C, Wang Z, Jiang J, Zhu C, Zhang N, Sun G, Zhang Q. Jiang C, et al. Front Microbiol. 2024 Jul 5;15:1416734. doi: 10.3389/fmicb.2024.1416734. eCollection 2024. Front Microbiol. 2024. PMID: 39035444 Free PMC article. - Amylase and Cellulase Production from Newly Isolated Bacillus subtilis Using Acid Treated Potato Peel Waste.
Mushtaq Q, Ishtiaq U, Joly N, Qazi JI, Martin P. Mushtaq Q, et al. Microorganisms. 2024 May 29;12(6):1106. doi: 10.3390/microorganisms12061106. Microorganisms. 2024. PMID: 38930488 Free PMC article. - Association between PDCD6-VNTR polymorphism and urinary cancer susceptibility.
Yang GE, Kim MH, Jeong MS, Lee SY, Choi YH, Nam JK, Kim TN, Leem SH. Yang GE, et al. Genes Genomics. 2024 Nov;46(11):1281-1291. doi: 10.1007/s13258-024-01523-9. Epub 2024 Jun 8. Genes Genomics. 2024. PMID: 38850471
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources