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Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei M, Gojobori T. Nei M, et al. Mol Biol Evol. 1986 Sep;3(5):418-26. doi: 10.1093/oxfordjournals.molbev.a040410. Mol Biol Evol. 1986. PMID: 3444411
Relative roles of mutation and selection in the maintenance of genetic variability.
Nei M. Nei M. Philos Trans R Soc Lond B Biol Sci. 1988 Jul 6;319(1196):615-29. doi: 10.1098/rstb.1988.0069. Philos Trans R Soc Lond B Biol Sci. 1988. PMID: 2905496
THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS.
Nei M, Maruyama T, Chakraborty R. Nei M, et al. Evolution. 1975 Mar;29(1):1-10. doi: 10.1111/j.1558-5646.1975.tb00807.x. Evolution. 1975. PMID: 28563291 No abstract available.
DEFINITION AND ESTIMATION OF FIXATION INDICES.
Nei M. Nei M. Evolution. 1986 May;40(3):643-645. doi: 10.1111/j.1558-5646.1986.tb00516.x. Evolution. 1986. PMID: 28556335 No abstract available.
BOTTLENECK EFFECTS ON AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE WITH THE STEPWISE MUTATION MODEL.
Chakraborty R, Nei M. Chakraborty R, et al. Among authors: nei m. Evolution. 1977 Jun;31(2):347-356. doi: 10.1111/j.1558-5646.1977.tb01017.x. Evolution. 1977. PMID: 28563234 No abstract available.
The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data.
Katsura Y, Stanley CE Jr, Kumar S, Nei M. Katsura Y, et al. Among authors: nei m. Mol Biol Evol. 2017 Mar 1;34(3):718-723. doi: 10.1093/molbev/msw272. Mol Biol Evol. 2017. PMID: 28100791 Free PMC article.
Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes.
Yoshida R, Nei M. Yoshida R, et al. Among authors: nei m. Mol Biol Evol. 2016 Jun;33(6):1618-24. doi: 10.1093/molbev/msw042. Epub 2016 Feb 28. Mol Biol Evol. 2016. PMID: 26929244
This c is given by Pc (1 - dT/dTmax) = Pc (m - 3 - dT/2)/(m - 3), where m is the number of taxa used and dTmax is the maximum possible value of dT, which is given by 2(m - 3). ...
This c is given by Pc (1 - dT/dTmax) = Pc (m - 3 - dT/2)/(m - 3), where m is the number of taxa used and dTmax is the m …
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. Among authors: nei m. 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.
POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface.
Takezaki N, Nei M, Tamura K. Takezaki N, et al. Among authors: nei m. Mol Biol Evol. 2010 Apr;27(4):747-52. doi: 10.1093/molbev/msp312. Epub 2009 Dec 18. Mol Biol Evol. 2010. PMID: 20022889 Free PMC article.
False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus.
Suzuki Y, Nei M. Suzuki Y, et al. Among authors: nei m. Mol Biol Evol. 2004 May;21(5):914-21. doi: 10.1093/molbev/msh098. Epub 2004 Mar 10. Mol Biol Evol. 2004. PMID: 15014169
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