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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Example Data

The following data files are included in the MEGA 4 installation package. They are provided as downloads for refrence purposes.
File Name
Sample trace file in ABI file format.
Protein coding genes from chloroplast genome of nine speices.
Human and Chimp contigs for genes/domains tutorial.

Sequences for gene encoding mitocondrial large-subunit ribosomal RNA.

Human mtDNA data 526.
Sample distance data file generated for six groups using Tamura-Nei method.

Adh sequence data from eleven fruit fly species.

Nucleotide sequences of three human class I HLA-A alleles.
Unaligned HSP20 sequence data for four species.

Genetic distance data from 15 human populations
Nei, M. and A. K. Roychoudhury. 1993. Mol. Biol. Evol. 10(5).

Sample tree topology for eight species in Newick file format.

Additional example data files related to Molecular Evolution and Phylogenetics by Nei and Kumar can be found at the book's supplementary data website.