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Items: 32

1.

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV.

Mol Biol Evol. 2019 Aug 27. pii: msz197. doi: 10.1093/molbev/msz197. [Epub ahead of print]

PMID:
31504749
2.

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

Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Mar 1;35(3):773-777. doi: 10.1093/molbev/msx335.

3.

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

Pattin KA, Greene AC, Altman RB, Cohen KB, Wethington E, Görg C, Hunter LE, Muse SV, Radivojac P, Moore JH.

Pac Symp Biocomput. 2015:488-92.

4.

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

Katz LA, DeBerardinis J, Hall MS, Kovner AM, Dunthorn M, Muse SV.

J Mol Evol. 2011 Dec;73(5-6):266-72. doi: 10.1007/s00239-011-9468-x. Epub 2012 Jan 19.

5.

CodonTest: modeling amino acid substitution preferences in coding sequences.

Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL.

PLoS Comput Biol. 2010 Aug 19;6(8). pii: e1000885. doi: 10.1371/journal.pcbi.1000885.

6.

Correcting the bias of empirical frequency parameter estimators in codon models.

Kosakovsky Pond S, Delport W, Muse SV, Scheffler K.

PLoS One. 2010 Jul 30;5(7):e11230. doi: 10.1371/journal.pone.0011230. Erratum in: PLoS One. 2014;9(8):e106200.

7.

Benchmarking multi-rate codon models.

Delport W, Scheffler K, Gravenor MB, Muse SV, Kosakovsky Pond S.

PLoS One. 2010 Jul 21;5(7):e11587. doi: 10.1371/journal.pone.0011587.

8.

Genomic analysis of closely related astroviruses.

Strain E, Kelley LA, Schultz-Cherry S, Muse SV, Koci MD.

J Virol. 2008 May;82(10):5099-103. doi: 10.1128/JVI.01993-07. Epub 2008 Mar 5.

9.

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

Kosakovsky Pond SL, Mannino FV, Gravenor MB, Muse SV, Frost SD.

Mol Biol Evol. 2007 Jan;24(1):159-70. Epub 2006 Oct 12.

PMID:
17038448
10.

Genome architecture drives protein evolution in ciliates.

Zufall RA, McGrath CL, Muse SV, Katz LA.

Mol Biol Evol. 2006 Sep;23(9):1681-7. Epub 2006 Jun 7.

PMID:
16760419
11.

Site-to-site variation of synonymous substitution rates.

Pond SK, Muse SV.

Mol Biol Evol. 2005 Dec;22(12):2375-85. Epub 2005 Aug 17.

PMID:
16107593
12.

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

Strain E, Muse SV.

J Mol Evol. 2005 Sep;61(3):325-32. Epub 2005 Jul 21.

PMID:
16044247
13.

PowerMarker: an integrated analysis environment for genetic marker analysis.

Liu K, Muse SV.

Bioinformatics. 2005 May 1;21(9):2128-9. Epub 2005 Feb 10.

PMID:
15705655
14.

Column sorting: rapid calculation of the phylogenetic likelihood function.

Kosakovsky Pond SL, Muse SV.

Syst Biol. 2004 Oct;53(5):685-92.

PMID:
15545249
15.

HyPhy: hypothesis testing using phylogenies.

Pond SL, Frost SD, Muse SV.

Bioinformatics. 2005 Mar 1;21(5):676-9. Epub 2004 Oct 27.

PMID:
15509596
16.

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

Katz LA, Bornstein JG, Lasek-Nesselquist E, Muse SV.

Mol Biol Evol. 2004 Mar;21(3):555-62. Epub 2003 Dec 23.

PMID:
14694079
17.

Evolution of duplicated alpha-tubulin genes in ciliates.

Israel RL, Kosakovsky Pond SL, Muse SV, Katz LA.

Evolution. 2002 Jun;56(6):1110-22.

PMID:
12144013
18.

Examining rates and patterns of nucleotide substitution in plants.

Muse SV.

Plant Mol Biol. 2000 Jan;42(1):25-43. Review.

PMID:
10688129
19.

Molecular evolution of type 1 serine/threonine protein phosphatases.

Lin Q, Buckler ES 4th, Muse SV, Walker JC.

Mol Phylogenet Evol. 1999 Jun;12(1):57-66.

PMID:
10222161
20.

Intragenic duplication and divergence in the spectrin superfamily of proteins.

Thomas GH, Newbern EC, Korte CC, Bales MA, Muse SV, Clark AG, Kiehart DP.

Mol Biol Evol. 1997 Dec;14(12):1285-95.

PMID:
9402739
21.

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

Gaut BS, Clark LG, Wendel JF, Muse SV.

Mol Biol Evol. 1997 Jul;14(7):769-77.

PMID:
9214750
23.
24.

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

Clark AG, Leicht BG, Muse SV.

Mol Biol Evol. 1996 Mar;13(3):471-82.

PMID:
8742636
25.

Estimating synonymous and nonsynonymous substitution rates.

Muse SV.

Mol Biol Evol. 1996 Jan;13(1):105-14.

PMID:
8583885
26.

Maintenance of pre-mRNA secondary structure by epistatic selection.

Kirby DA, Muse SV, Stephan W.

Proc Natl Acad Sci U S A. 1995 Sep 26;92(20):9047-51.

27.
28.

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

Leicht BG, Muse SV, Hanczyc M, Clark AG.

Genetics. 1995 Jan;139(1):299-308.

30.

Relative rates of nucleotide substitution in the chloroplast genome.

Gaut BS, Muse SV, Clegg MT.

Mol Phylogenet Evol. 1993 Jun;2(2):89-96. Erratum in: Mol Phylogenet Evol 1994 Jun;3(2):185. Mol Phylogenet Evol 1994 Mar;3(1):83.

PMID:
8043149
31.

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

Gaut BS, Muse SV, Clark WD, Clegg MT.

J Mol Evol. 1992 Oct;35(4):292-303.

PMID:
1404415
32.

Testing for equality of evolutionary rates.

Muse SV, Weir BS.

Genetics. 1992 Sep;132(1):269-76.

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