Synonymous and nonsynonymous rate variation in nuclear genes of mammals
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Cameron JM (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J Mol Evol 41: 1152–1159
Easteal S, Collet C (1994) Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral. Mol Biol Evol 11:643–647
Eyre-Walker A, Gaut BS (1997) Correlated rates of synonymous site evolution across plant genomes. Mol Biol Evol 14:455–460
Gillespie JH (1987) Molecular evolution and the neutral allele theory. Oxf Surv Evol Biol 4:10–37
Gillespie JH (1989) Lineage effects and the index of dispersion of molecular evolution. Mol Biol Evol 6:636–647
Gillespie JH (1991) The causes of molecular evolution. Oxford University Press, Oxford
Goldman N (1994) Variance to mean ratio, R(t), for Poisson processes on phylogenetic trees. Mol Phylogenet Evol 3:230–239
Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725–736
Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862–864
Ina Y (1995) Amino acid difference formula to help explain protein evolution. Science 185:862–864
Ina Y (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J Mol Evol 40:190–226
Ina Y (1996) Patterns of synonymous and nonsynonymous substitutions: an indicator of mechanisms of molecular evolution. J Genet 75:91–115
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96–99
Li W-H, Wu C-I, Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174
McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652–654
Miyata T, Yasunaga T (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its applications. J Mol Evol 16:23–36
Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to chloroplast genome. Mol Biol Evol 11:715–724
Nei M, Gojobori T (1986) Simple methods for estimating the number of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
Nielsen R (1997) Robustness of the estimator of the index of dispersion for DNA sequences. Mol Phylogenet Evol 7:346–351
Ohta T (1993) A examination of the generation-time effect on molecular evolution. Proc Natl Acad Sci USA 90:10676–10680
Ohta T (1995) Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol 40:56–63
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes- rates and interdependence between the genes. Mol Biol Evol 10: 271–281
Yang Z (1997) Phylogenetic analysis by maximum likelihood (PAML), version 1.3. University of California, Berkeley, California, USA