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List of works by Spencer V Muse

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

scientific article (publication date: September 1994)

Benchmarking multi-rate codon models

scientific article

CodonTest: modeling amino acid substitution preferences in coding sequences

scientific article

Column sorting: rapid calculation of the phylogenetic likelihood function

scientific article published in October 2004

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

scientific article

Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae) ⬇️

scientific article published on July 1, 1997

Comparisons of the nucleotide substitution process among repetitive segments of the alpha- and beta-spectrin genes

scientific article

Constraints on intron evolution in the gene encoding the myosin alkali light chain in Drosophila

scientific article

Correcting the bias of empirical frequency parameter estimators in codon models

scientific article

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes

scientific article published on 2 January 2018

Development of a maize molecular evolutionary genomic database

scientific article published on January 2003

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

scientific article published on 23 December 2003

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

scientific article published on 02 March 2020

Evolution of duplicated alpha-tubulin genes in ciliates

scientific article

Evolutionary model selection with a genetic algorithm: a case study using stem RNA.

scientific article published on 12 October 2006

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

scientific article

Genome architecture drives protein evolution in ciliates

scientific article published on 07 June 2006

Genomic analysis of closely related astroviruses

scientific article published on 5 March 2008

Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata.

scientific article published on December 2011

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

scientific article published on 01 January 2020

HyPhy: Hypothesis Testing Using Phylogenies

scholarly article

HyPhy: hypothesis testing using phylogenies

scientific article (publication date: 27 October 2004)

Intragenic duplication and divergence in the spectrin superfamily of proteins ⬇️

scientific article published on 01 December 1997

Length variation and secondary structure of introns in the Mlc1 gene in six species of Drosophila

scientific article published in March 1996

Molecular Evolution of Type 1 Serine/Threonine Protein Phosphatases

article

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

scientific article published on 21 July 2005

PowerMarker: an integrated analysis environment for genetic marker analysis

scientific article published on 10 February 2005

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

scientific article published on October 1, 1992

Relative rates of nucleotide substitution in the chloroplast genome.

scientific article published in June 1993

Site-to-site variation of synonymous substitution rates

scientific article

Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: ignore at your own peril

scientific article published on 18 February 2020

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

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