Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes von Weaver, Steven, Shank, Stephen D, Spielman, Stephanie J, Li, Michael, Muse, Spencer V, Kosakovsky Pond, Sergei L

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HyPhy: hypothesis testing using phylogenies von Pond, Sergei L. Kosakovsky, Frost, Simon D. W., Muse, Spencer V.

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Site-to-site variation of synonymous substitution rates von Pond, Sergei Kosakovsky, Muse, Spencer V

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Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability von Mannino, Frank, Wisotsky, Sadie, Pond, Sergei L. Kosakovsky, Muse, Spencer

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies von Kosakovsky Pond, Sergei L, Poon, Art F Y, Velazquez, Ryan, Weaver, Steven, Hepler, N Lance, Murrell, Ben, Shank, Stephen D, Magalis, Brittany Rife, Bouvier, Dave, Nekrutenko, Anton, Wisotsky, Sadie, Spielman, Stephanie J, Frost, Simon D W, Muse, Spencer V

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CodonTest: modeling amino acid substitution preferences in coding sequences von Delport, Wayne, Scheffler, Konrad, Botha, Gordon, Gravenor, Mike B, Muse, Spencer V, Kosakovsky Pond, Sergei L

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Correcting the bias of empirical frequency parameter estimators in codon models von Kosakovsky Pond, Sergei, Delport, Wayne, Muse, Spencer V, Scheffler, Konrad

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Genomic Analysis of Closely Related Astroviruses von STRAIN, Errol, KELLEY, Laura A, SCHULTZ-CHERRY, Stacey, MUSE, Spencer V, KOCI, Matthew D

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PowerMarker: an integrated analysis environment for genetic marker analysis von Liu, Kejun, Muse, Spencer V.

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Genome architecture drives protein evolution in ciliates von Zufall, Rebecca A, McGrath, Casey L, Muse, Spencer V, Katz, Laura A

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Benchmarking multi-rate codon models von Delport, Wayne, Scheffler, Konrad, Gravenor, Mike B, Muse, Spencer V, Kosakovsky Pond, Sergei

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Heterogeneous Rates of Molecular Evolution Among Cryptic Species of the Ciliate Morphospecies Chilodonella uncinata von Katz, Laura A., DeBerardinis, Jennifer, Hall, Meaghan S., Kovner, Alexandra M., Dunthorn, Micah, Muse, Spencer V.

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Examining rates and patterns of nucleotide substitution in plants von Muse, S V

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Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril von Wisotsky, Sadie R., Pond, Sergei L. Kosakovsky, Shank, Stephen D., Muse, Spencer

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Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes von Katz, Laura A, Bornstein, Jacob G, Lasek-Nesselquist, Erica, Muse, Spencer V

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Positively selected sites in the Arabidopsis receptor-like kinase gene family von Strain, Errol, Muse, Spencer V

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Evolutionary Model Selection with a Genetic Algorithm: A Case Study Using Stem RNA von Kosakovsky Pond, Sergei L., Mannino, Frank V., Gravenor, Michael B., Muse, Spencer V., Frost, Simon D. W.

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Column Sorting: Rapid Calculation of the Phylogenetic Likelihood Function von Pond, Sergei L. Kosakovsky, Muse, Spencer V., Huelsenbeck, John

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Maintenance of pre-mRNA secondary structure by epistatic selection von Kirby, D.A, Muse, S.V, Stephan, W

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Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants von Gaut, B.S, Muse, S.V, Clark, W.D, Clegg, M.T

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