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Items: 1 to 20 of 133


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.


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.


Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

Miyazawa S.

PLoS One. 2011;6(12):e28892. doi: 10.1371/journal.pone.0028892. Epub 2011 Dec 29.


A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny.

Wang HC, Li K, Susko E, Roger AJ.

BMC Evol Biol. 2008 Dec 16;8:331. doi: 10.1186/1471-2148-8-331.


An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.

Wang HC, Susko E, Roger AJ.

Mol Biol Evol. 2014 Apr;31(4):779-92. doi: 10.1093/molbev/msu044. Epub 2014 Jan 16.


Empirical models for substitution in ribosomal RNA.

Smith AD, Lui TW, Tillier ER.

Mol Biol Evol. 2004 Mar;21(3):419-27. Epub 2003 Dec 5.


A generalized mechanistic codon model.

Zaheri M, Dib L, Salamin N.

Mol Biol Evol. 2014 Sep;31(9):2528-41. doi: 10.1093/molbev/msu196. Epub 2014 Jun 23.


Phylogenetic estimation of context-dependent substitution rates by maximum likelihood.

Siepel A, Haussler D.

Mol Biol Evol. 2004 Mar;21(3):468-88. Epub 2003 Dec 5.


Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.


Bayesian analysis of amino acid substitution models.

Huelsenbeck JP, Joyce P, Lakner C, Ronquist F.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3941-53. doi: 10.1098/rstb.2008.0175.


Superiority of a mechanistic codon substitution model even for protein sequences in phylogenetic analysis.

Miyazawa S.

BMC Evol Biol. 2013 Nov 21;13:257. doi: 10.1186/1471-2148-13-257.


Pseudo-likelihood for non-reversible nucleotide substitution models with neighbour dependent rates.

Christensen OF.

Stat Appl Genet Mol Biol. 2006;5:Article18. Epub 2006 Jul 31.


Evolutionary fingerprinting of genes.

Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD.

Mol Biol Evol. 2010 Mar;27(3):520-36. doi: 10.1093/molbev/msp260. Epub 2009 Oct 28.


Codon substitution models based on residue similarity and their applications.

Liu X, Liu H, Guo W, Yu K.

Gene. 2012 Nov 1;509(1):136-41. doi: 10.1016/j.gene.2012.07.075. Epub 2012 Aug 10.


Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.


Models of amino acid substitution and applications to mitochondrial protein evolution.

Yang Z, Nielsen R, Hasegawa M.

Mol Biol Evol. 1998 Dec;15(12):1600-11.


Improving phylogenetic inference with a semiempirical amino acid substitution model.

Zoller S, Schneider A.

Mol Biol Evol. 2013 Feb;30(2):469-79. doi: 10.1093/molbev/mss229. Epub 2012 Sep 21.


Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

Holder MT, Zwickl DJ, Dessimoz C.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4013-21. doi: 10.1098/rstb.2008.0162.

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