Format
Sort by

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 113

1.

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.

2.

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.

PMID:
22902303
3.

Estimating empirical codon hidden Markov models.

De Maio N, Holmes I, Schlötterer C, Kosiol C.

Mol Biol Evol. 2013 Mar;30(3):725-36. doi: 10.1093/molbev/mss266. Epub 2012 Nov 27.

4.

An empirical codon model for protein sequence evolution.

Kosiol C, Holmes I, Goldman N.

Mol Biol Evol. 2007 Jul;24(7):1464-79. Epub 2007 Mar 30. Erratum in: Mol Biol Evol. 2007 Sep;24(9):2151.

5.

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.

6.

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.

7.

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.

8.

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.

9.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

10.

A combined empirical and mechanistic codon model.

Doron-Faigenboim A, Pupko T.

Mol Biol Evol. 2007 Feb;24(2):388-97. Epub 2006 Nov 16.

11.

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

Aris-Brosou S, Bielawski JP.

Gene. 2006 Aug 15;378:58-64. Epub 2006 May 22.

PMID:
16797879
12.
13.

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.

15.

Empirical analysis of the most relevant parameters of codon substitution models.

Zoller S, Schneider A.

J Mol Evol. 2010 Jun;70(6):605-12. doi: 10.1007/s00239-010-9356-9. Epub 2010 Jun 5.

PMID:
20526712
17.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Goldman N, Yang Z.

Mol Biol Evol. 1994 Sep;11(5):725-36.

PMID:
7968486
18.

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

Christensen OF, Hobolth A, Jensen JL.

J Comput Biol. 2005 Nov;12(9):1166-82.

PMID:
16305327
19.

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.

20.

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.

Items per page

Supplemental Content

Write to the Help Desk