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Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Molecular biology and evolution, 2018-03, Vol.35 (3), p.773-777

2018

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HyPhy: hypothesis testing using phylogenies

Bioinformatics, 2005-03, Vol.21 (5), p.676-679

2005

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Site-to-site variation of synonymous substitution rates

Molecular biology and evolution, 2005-12, Vol.22 (12), p.2375-2385

2005

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Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability

PloS one, 2020-03, Vol.15 (3), p.e0229493

2020

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Molecular biology and evolution, 2020-01, Vol.37 (1), p.295-299

2020

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CodonTest: modeling amino acid substitution preferences in coding sequences

PLoS computational biology, 2010-08, Vol.6 (8), p.e1000885

2010

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Correcting the bias of empirical frequency parameter estimators in codon models

PloS one, 2010-07, Vol.5 (7), p.e11230-e11230

2010

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Genomic Analysis of Closely Related Astroviruses

Journal of Virology, 2008-05, Vol.82 (10), p.5099-5103

2008

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PowerMarker: an integrated analysis environment for genetic marker analysis

Bioinformatics, 2005-05, Vol.21 (9), p.2128-2129

2005

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Genome architecture drives protein evolution in ciliates

Molecular biology and evolution, 2006-09, Vol.23 (9), p.1681-1687

2006

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Benchmarking multi-rate codon models

PloS one, 2010-07, Vol.5 (7), p.e11587-e11587

2010

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Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata

Journal of molecular evolution, 2011-12, Vol.73 (5-6), p.266-272

2011

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Examining rates and patterns of nucleotide substitution in plants

Plant molecular biology, 2000-01, Vol.42 (1), p.25-43

Muse, S V

2000

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Training the next generation of quantitative biologists in the era of big data

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2015, p.488

2015

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Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril

Molecular biology and evolution, 2020-08, Vol.37 (8), p.2430-2439

2020

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Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes

Molecular biology and evolution, 2004-03, Vol.21 (3), p.555-562

2004

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Positively selected sites in the Arabidopsis receptor-like kinase gene family

Journal of molecular evolution, 2005-09, Vol.61 (3), p.325-332

2005

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Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA

Molecular biology and evolution, 2007-01, Vol.24 (1), p.159-170

2007

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Column Sorting: Rapid Calculation of the Phylogenetic Likelihood Function

Systematic biology, 2004-10, Vol.53 (5), p.685-692

2004

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Maintenance of pre-mRNA secondary structure by epistatic selection

Proceedings of the National Academy of Sciences - PNAS, 1995-09, Vol.92 (20), p.9047-9051

1995

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Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants

Journal of molecular evolution, 1992-10, Vol.35 (4), p.292-303

1992

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EVOLUTION OF DUPLICATED ALPHA-TUBULIN GENES IN CILIATES

Evolution, 2002-06, Vol.56 (6), p.1110-1122, Article 1110

2002

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Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test

Genetics (Austin), 1997-05, Vol.146 (1), p.393-399

1997

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

Molecular biology and evolution, 1994-09, Vol.11 (5), p.715-724

1994

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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences: e1000885

PLoS computational biology, 2010-08, Vol.6 (8)

2010

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Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

HyPhy: hypothesis testing using phylogenies

Site-to-site variation of synonymous substitution rates

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

CodonTest: modeling amino acid substitution preferences in coding sequences

Correcting the bias of empirical frequency parameter estimators in codon models

Genomic Analysis of Closely Related Astroviruses

PowerMarker: an integrated analysis environment for genetic marker analysis

Genome architecture drives protein evolution in ciliates

Benchmarking multi-rate codon models

Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata

Examining rates and patterns of nucleotide substitution in plants

Training the next generation of quantitative biologists in the era of big data

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril

Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes

Positively selected sites in the Arabidopsis receptor-like kinase gene family

Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA

Column Sorting: Rapid Calculation of the Phylogenetic Likelihood Function

Maintenance of pre-mRNA secondary structure by epistatic selection

Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants

EVOLUTION OF DUPLICATED ALPHA-TUBULIN GENES IN CILIATES

Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test

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

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences: e1000885

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