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Items: 1 to 20 of 99

1.

Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V.

PLoS One. 2012;7(3):e33852. doi: 10.1371/journal.pone.0033852. Epub 2012 Mar 27.

2.

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.

3.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages.

Jayaswal V, Wong TK, Robinson J, Poladian L, Jermiin LS.

Syst Biol. 2014 Sep;63(5):726-42. doi: 10.1093/sysbio/syu036. Epub 2014 Jun 12.

PMID:
24927722
4.

Efficient selection of branch-specific models of sequence evolution.

Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B.

Mol Biol Evol. 2012 Jul;29(7):1861-74. doi: 10.1093/molbev/mss059. Epub 2012 Feb 2.

PMID:
22319139
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.

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference.

Roure B, Philippe H.

BMC Evol Biol. 2011 Jan 14;11:17. doi: 10.1186/1471-2148-11-17.

7.

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.

Matsumoto T, Akashi H, Yang Z.

Genetics. 2015 Jul;200(3):873-90. doi: 10.1534/genetics.115.177386. Epub 2015 May 6.

8.

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.

9.

Tree and rate estimation by local evaluation of heterochronous nucleotide data.

Yang Z, O'Brien JD, Zheng X, Zhu HQ, She ZS.

Bioinformatics. 2007 Jan 15;23(2):169-76. Epub 2006 Nov 16.

PMID:
17110369
10.

Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias.

Liu Y, Cox CJ, Wang W, Goffinet B.

Syst Biol. 2014 Nov;63(6):862-78. doi: 10.1093/sysbio/syu049. Epub 2014 Jul 28.

PMID:
25070972
11.

Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster.

Singh ND, Arndt PF, Petrov DA.

Genetics. 2005 Feb;169(2):709-22. Epub 2004 Nov 1.

12.

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.

PMID:
14660689
13.

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.

Lartillot N, Philippe H.

Mol Biol Evol. 2004 Jun;21(6):1095-109. Epub 2004 Mar 10.

PMID:
15014145
15.

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates.

Garamszegi LZ, de Groot NG, Bontrop RE.

BMC Evol Biol. 2009 Apr 12;9:73. doi: 10.1186/1471-2148-9-73.

16.

The genetic code can cause systematic bias in simple phylogenetic models.

Whelan S.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4003-11. doi: 10.1098/rstb.2008.0171.

17.

Phylogenetic analysis using parsimony and likelihood methods.

Yang Z.

J Mol Evol. 1996 Feb;42(2):294-307.

PMID:
8919881
18.

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.

PMID:
9866196
19.

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models.

Tsagkogeorga G, Turon X, Hopcroft RR, Tilak MK, Feldstein T, Shenkar N, Loya Y, Huchon D, Douzery EJ, Delsuc F.

BMC Evol Biol. 2009 Aug 5;9:187. doi: 10.1186/1471-2148-9-187.

20.

A site- and time-heterogeneous model of amino acid replacement.

Blanquart S, Lartillot N.

Mol Biol Evol. 2008 May;25(5):842-58. doi: 10.1093/molbev/msn018. Epub 2008 Jan 29.

PMID:
18234708

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