MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

1987 • 59,130 citations

Estimating the Dimension of a Model

1978 • 43,634 citations

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

1985 • 39,646 citations

MODELTEST: testing the model of DNA substitution.

1998 • 20,214 citations

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

2003 • 16,546 citations

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

2010 • 16,332 citations

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

2006 • 15,367 citations

Evolutionary trees from DNA sequences: A maximum likelihood approach

1981 • 14,097 citations

PAUP^* : Phylogenetic Analysis Using Parsimony (and other methods) 4.0b8

2001 • 13,157 citations

Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.

1993 • 10,775 citations

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

1985 • 8,642 citations

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

2004 • 8,303 citations

Molecular Evolution and Phylogenetics

2000 • 7,148 citations

The rapid generation of mutation data matrices from protein sequences

1992 • 6,766 citations

Regression and time series model selection in small samples

1989 • 5,837 citations

Prospects for inferring very large phylogenies by using the neighbor-joining method

2004 • 5,025 citations

MOLECULAR BIOLOGY AND EVOLUTION

2021 • 4,185 citations

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

2004 • 3,811 citations

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

2008 • 3,414 citations

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

1994 • 2,921 citations

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

1997 • 1,731 citations

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

1997 • 1,675 citations

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

2004 • 1,450 citations

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers

1994 • 1,092 citations

Simple methods for testing the molecular evolutionary clock hypothesis.

1993 • 951 citations

Phylogenetic test of the molecular clock and linearized trees.

1995 • 837 citations

Computational Molecular Evolution

2006 • 823 citations

A new method of inference of ancestral nucleotide and amino acid sequences.

1995 • 725 citations

The timetree of life

2009 • 588 citations

Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791

1985 • 491 citations

Incomplete taxon sampling is not a problem for phylogenetic inference

2001 • 333 citations

Progress in Clinical and Biological Research

1983 • 206 citations

Likelihood. An Account of the Statistical Concept of Likelihood and Its Application to Scientific Inference.

1973 • 204 citations

A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case

1967 • 156 citations

Does Choice in Model Selection Affect Maximum Likelihood Analysis?

2008 • 138 citations

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated.

1989 • 97 citations

Heterogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference

2003 • 93 citations

Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty

2006 • 89 citations

Bioinformatics software for biologists in the genomics era

2007 • 79 citations

Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods

2010 • 51 citations

Discovering the Timetree of Life

2009 • 47 citations

Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

2005 • 36 citations

Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times

2011 • 35 citations

An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor.

1986 • 23 citations

An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping.

2006 • 5 citations