Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites

The rapid generation of mutation data matrices from protein sequences

1992 • 6,766 citations

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

1994 • 2,921 citations

A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

2001 • 2,762 citations

Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies

1996 • 2,613 citations

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

1997 • 1,675 citations

A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process

2004 • 1,500 citations

Among-site rate variation and its impact on phylogenetic analyses

1996 • 1,204 citations

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.

1993 • 1,064 citations

A Hidden Markov Model approach to variation among sites in rate of evolution

1996 • 839 citations

Algorithm AS 183: An Efficient and Portable Pseudo-Random Number Generator

1982 • 624 citations

Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues

2002 • 607 citations

Statistical methods for testing functional divergence after gene duplication

1999 • 444 citations

Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior

2004 • 442 citations

A space-time process model for the evolution of DNA sequences.

1995 • 409 citations

Heterotachy, an Important Process of Protein Evolution

2002 • 351 citations

Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies

1998 • 335 citations

Maximum-Likelihood Approach for Gene Family Evolution Under Functional Divergence

2001 • 303 citations

DIVERGE: phylogeny-based analysis for functional–structural divergence of a protein family

2002 • 279 citations

Rose: generating sequence families.

1998 • 277 citations

Coevolving protein residues: maximum likelihood identification and relationship to structure 1 1Edited by G. Von Heijne

1999 • 244 citations

CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content

2004 • 214 citations

The Effect of Taxon Sampling on Estimating Rate Heterogeneity Parameters of Maximum-Likelihood Models

1999 • 194 citations

The Influence of Mutation, Recombination, Population History, and Selection on Patterns of Genetic Diversity in Neisseria meningitidis

2004 • 153 citations

A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins

2001 • 150 citations

Predicting functional divergence in protein evolution by site-specific rate shifts

2002 • 147 citations

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages

1998 • 141 citations

Modeling residue usage in aligned protein sequences via maximum likelihood

1996 • 117 citations

Functional Divergence in the Caspase Gene Family and Altered Functional Constraints: Statistical Analysis and Prediction

2001 • 115 citations

Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle

2004 • 97 citations

Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data

2004 • 92 citations

Accounting for Uncertainty in the Tree Topology Has Little Effect on the Decision-Theoretic Approach to Model Selection in Phylogeny Estimation

2004 • 88 citations

Invariable Sites Models and Their Use in Phylogeny Reconstruction

2000 • 84 citations

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes

2002 • 72 citations

The Pattern of Amino Acid Replacements in α/β-Barrels

2002 • 67 citations

Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity

2002 • 67 citations

Naturally Occurring Transposable Elements Disrupt hsp70 Promoter Function in Drosophila melanogaster

2004 • 65 citations

Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models

2003 • 63 citations

Testing for Differences in Rates-Across-Sites Distributions in Phylogenetic Subtrees

2002 • 56 citations

Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny

2000 • 49 citations

Heterotachy and Functional Shift in Protein Evolution

2003 • 46 citations

An Empirical Analysis of mt 16S rRNA Covarion-Like Evolution in Insects: Site-Specific Rate Variation Is Clustered and Frequently Detected

2002 • 40 citations

Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information

2003 • 38 citations

Assessing functional divergence in EF-1 and its paralogs in eukaryotes and archaebacteria

2003 • 33 citations

The Cellular Retinol-Binding Protein Genes Are Duplicated and Differentially Transcribed in the Developing and Adult Zebrafish (Danio rerio)

2004 • 30 citations

PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees

1997 • 28 citations

Lack of Evidence for Horizontal Transfer of the lac Operon into Escherichia coli

2004 • 27 citations

CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints

2002 • 11 citations