MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

Briefings in Bioinformatics

Volumn 9, Issue 4, 2008, Pages 299-306

  Kumar, Sudhir ^a   Nei, Masatoshi ^b   Dudley, Joel ^c   Tamura, Koichiro ^d  

^a ARIZONA STATE UNIVERSITY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

Evolution; Genome; Phylogenetics; Software

Indexed keywords

DNA; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA SEQUENCE; EVOLUTIONARY ALGORITHM; GENETIC ANALYSIS; INTERNET; MAXIMUM LIKELIHOOD METHOD; MEDICAL RESEARCH; MULTIGENE FAMILY; PHYLOGENETIC TREE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STATISTICAL ANALYSIS;

ALGORITHMS; BASE SEQUENCE; BIOLOGY; CHROMOSOME MAPPING; DNA; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; VARIATION (GENETICS);

EID: 45949109669     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn017     Document Type: Article

References (16)

1. Swofford D. PAUP: Phylogenetic Analysis Using Maximum Parsimony. Illinois: Illinois Natural History Survey Champaign, 1990.
2. Felsenstein J. PHYLIP: Phylogenetic Inference Package. Seattle, WA: University of Washington, 1993.
3. Felsenstein J. Inferring phylogenies. Sunderland, MA: Sinauer Associates, 2004.
4. Nei M. Molecular Evolutionary Genetics. New York: Columbia University Press, 1987.
5. Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York: Oxford, University Press, 2000.
6. Yang Z. Computational Molecular Evolution. Oxford: Oxford University Press, 2006.
7. Kumar S, Tamura K, Nei M. Manual for MEGA: Molecular Evolutionary Genetics Analysis Software. University Park, PA: Pennsylvania State University, 1993.
8. Kumar S, Tamura K, Nei M. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput Appl Biosci 1994;10 189-91.
9. Saitou N, Nei M. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4 406-25.
10. Kumar S, Dudley J. Bioinformatics software for biologists in the genomics era. Bioinformatics 2007;23:1713-7.
11. Kumar S, Tamura K, Jakobsen IB, et al. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 2001; 17:1244-5.
12. Kumar S, Tamura K, Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 2004;5:150-63.
13. Tamura K, Dudley J, Nei M, et al. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-9.
14. Takezaki N, Rzhetsky A, Nei M. Phylogenetic test of the molecular clock and linearized trees. Mol Biol Evol 1995;12: 823-33.
15. Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods Enzymol 1996; 266:383-402.
16. Hall BG. Phylogenetic trees made easy: A how-to manual. Sunderland, MA: Sinauer Associates, 2007.