Building phylogenetic trees from molecular data with MEGA

Molecular Biology and Evolution

Volumn 30, Issue 5, 2013, Pages 1229-1235

  Hall, Barry G ^a  

^a Bellingham Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; EVOLUTIONARY ALGORITHM; GENETIC ANALYSIS; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; SEQUENCE ANALYSIS;

ALGORITHMS; EVOLUTION, MOLECULAR; INTERNET; PHYLOGENY; SOFTWARE;

EID: 84876533617     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst012     Document Type: Article

References (13)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res. 25: 3389-3402. (Pubitemid 27359211)
2. Edgar RC. 2004a. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
3. Edgar RC. 2004b. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. (Pubitemid 38832724)
4. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates.
5. Gouy M, Guindon S, Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 27: 221-224.
6. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59: 307-321.
7. Hall BG. 2011. Phylogenetic trees made easy: a how-to manual. 4th ed. Sunderland (MA): Sinauer Associates.
8. Hall BG, Barlow M. 2006. Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases. Ann Epidemiol. 16: 157-169. (Pubitemid 43259536)
9. Hall BG, Pikis A, Thompson J. 2009. Evolution and biochemistry of family 4 glycosidases: implications for assigning enzyme function in sequence annotations. Mol Biol Evol. 26: 2487-2497.
10. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. New York: Oxford University Press.
11. Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. 2010. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38(Web Server issue): W23-W28.
12. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28: 2731-2739.
13. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. (Pubitemid 24354800)