Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
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Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
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Links

Other Bioinformatics Software and Tools
MEP Computer Programs
PhyLip
PHYML
PAML

Book by Nei and Kumar
Oxford University Press Site for Molecular Evolution and Phylogenetics
Example Data Files from Molecular Evolution and Phylogenetics

Author Websites
Sudhir Kumar Laboratory of Evolutionary Functional Genomics
Koichiro Tamura TMU Evolutionary Genetics Laboratory
Masatoshi Nei Laboratory of Masatoshi Nei