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Items: 1 to 20 of 111

1.

Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences.

Baele G, Peer YV, Vansteelandt S.

BMC Evol Biol. 2009 Apr 30;9:87. doi: 10.1186/1471-2148-9-87.

2.

Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

BMC Evol Biol. 2010 Aug 10;10:244. doi: 10.1186/1471-2148-10-244.

3.

Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

J Mol Evol. 2010 Jul;71(1):34-50. doi: 10.1007/s00239-010-9362-y. Epub 2010 Jul 11.

PMID:
20623275
4.

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution.

Baele G, Lemey P, Vansteelandt S.

BMC Bioinformatics. 2013 Mar 6;14:85. doi: 10.1186/1471-2105-14-85.

5.

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences.

Baele G, Van de Peer Y, Vansteelandt S.

Syst Biol. 2008 Oct;57(5):675-92. doi: 10.1080/10635150802422324.

PMID:
18853356
6.

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes.

Baele G, Van de Peer Y, Vansteelandt S.

BMC Evol Biol. 2011 May 27;11:145. doi: 10.1186/1471-2148-11-145.

7.

Identifiability of parameters in MCMC Bayesian inference of phylogeny.

Rannala B.

Syst Biol. 2002 Oct;51(5):754-60.

PMID:
12396589
8.

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.

9.

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

Rodrigue N, Kleinman CL, Philippe H, Lartillot N.

Mol Biol Evol. 2009 Jul;26(7):1663-76. doi: 10.1093/molbev/msp078. Epub 2009 Apr 21.

10.

Fast optimization of statistical potentials for structurally constrained phylogenetic models.

Bonnard C, Kleinman CL, Rodrigue N, Lartillot N.

BMC Evol Biol. 2009 Sep 9;9:227. doi: 10.1186/1471-2148-9-227.

11.

Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards.

Castoe TA, Doan TM, Parkinson CL.

Syst Biol. 2004 Jun;53(3):448-69.

PMID:
15503673
12.

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

dos Reis M, Yang Z.

Mol Biol Evol. 2011 Jul;28(7):2161-72. doi: 10.1093/molbev/msr045. Epub 2011 Feb 10.

13.

Bayesian phylogenetic analysis of combined data.

Nylander JA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL.

Syst Biol. 2004 Feb;53(1):47-67.

PMID:
14965900
15.

A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model.

Gowri-Shankar V, Rattray M.

Mol Biol Evol. 2007 Jun;24(6):1286-99. Epub 2007 Mar 7.

17.

Bayesian model adequacy and choice in phylogenetics.

Bollback JP.

Mol Biol Evol. 2002 Jul;19(7):1171-80.

18.

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.

Dutheil J, Boussau B.

BMC Evol Biol. 2008 Sep 22;8:255. doi: 10.1186/1471-2148-8-255.

20.

Assessing site-interdependent phylogenetic models of sequence evolution.

Rodrigue N, Philippe H, Lartillot N.

Mol Biol Evol. 2006 Sep;23(9):1762-75. Epub 2006 Jun 20.

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