Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

A new look at the statistical model identification

1974 • 46,507 citations

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

1980 • 28,067 citations

Evolutionary trees from DNA sequences: A maximum likelihood approach

1981 • 14,097 citations

The Neutral Theory of Molecular Evolution

1979 • 7,965 citations

The Neutral Theory of Molecular Evolution

1983 • 6,141 citations

PAML: a program package for phylogenetic analysis by maximum likelihood

1997 • 5,344 citations

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

1986 • 4,940 citations

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods

1994 • 2,921 citations

Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions

1987 • 2,429 citations

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

1994 • 2,001 citations

Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection

1988 • 1,968 citations

A Test of Neutral Molecular Evolution Based on Nucleotide Data

1987 • 1,789 citations

Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene

1998 • 1,615 citations

Phylogeny of the Genus Flavivirus

1998 • 1,064 citations

The Nearly Neutral Theory of Molecular Evolution

1992 • 1,052 citations

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.

1994 • 942 citations

Statistical tests of models of DNA substitution

1993 • 785 citations

Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

1995 • 554 citations

Episodic adaptive evolution of primate lysozymes

1997 • 476 citations

Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application

1980 • 404 citations

Long term trends in the evolution of H(3) HA1 human influenza type A

1997 • 403 citations

HIV-1 Regulatory/Accessory Genes: Keys to Unraveling Viral and Host Cell Biology

1998 • 392 citations

Large-scale search for genes on which positive selection may operate

1996 • 367 citations

Population dynamics of flaviviruses revealed by molecular phylogenies.

1996 • 348 citations

Models of Molecular Evolution and Phylogeny: Table 1.

1998 • 286 citations

Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders

1998 • 233 citations

Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection

1999 • 172 citations

Coalescing into the 21st Century: An Overview and Prospects of Coalescent Theory

1999 • 154 citations

Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history

1997 • 133 citations

Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).

1995 • 130 citations

Genealogical Evidence for Positive Selection in the nef Gene of HIV-1

1999 • 127 citations

Within- and between-species DNA sequence variation and the ‘footprint’ of natural selection

1999 • 115 citations

Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

1996 • 99 citations

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts

1997 • 98 citations

Statistical tests of neutrality in the age of weak selection

1998 • 94 citations

Algorithm AS 63: The Incomplete Beta Integral

1973 • 89 citations

The Molecular Epidemiology Of Human Immunodeficiency Virus Type 1 In Edinburgh

1995 • 84 citations

Algorithm AS 32: The Incomplete Gamma Integral

1970 • 53 citations

Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees.

1996 • 51 citations

A codon-based model designed to describe lentiviral evolution

1998 • 44 citations

The ratio of replacement to silent divergence and tests of neutrality

1997 • 22 citations

The ratio of replacement to silent divergence and tests of neutrality

1997 • 17 citations