Phylogenetics, likelihood, evolution and complexity

Bioinformatics

Volumn 28, Issue 22, 2012, Pages 2989-2990

  De Koning, A P Jason ^a,b   Gu, Wanjun ^c   Castoe, Todd A ^a,d   Pollock, David D ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALGARY   (Canada)

^c Southeast University   (China)

^d UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY;

ALGORITHMS; ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; MARKOV CHAINS; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; SOFTWARE;

EID: 84869397994     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts555     Document Type: Article

References (10)

1. de Koning, A.P.J. et al. (2010) Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol. Biol. Evol., 27, 249-265.
2. Drummond, A.J. and Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol., 7, 214.
3. Faith, J.J. and Pollock, D.D. (2003) Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics, 165, 735-745. (Pubitemid 37337639)
4. Lartillot, N. (2006) Conjugate Gibbs sampling for Bayesian phylogenetic models. J. Comput. Biol., 13, 1701-1722. (Pubitemid 46175705)
5. Lartillot, N. et al. (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics, 25, 2286-2288.
6. Lartillot, N. and Philippe, H. (2006) Computing Bayes factors using thermodynamic integration. Syst. Biol., 55, 195-207. (Pubitemid 43355101)
7. Neal, R.M. (2003) Slice sampling. Ann. Stat., 31, 705-741. (Pubitemid 38640403)
8. Rodrigue, N. and Aris-Brosou, S. (2011) Fast Bayesian choice of phylogenetic models: prospecting data augmentation-based thermodynamic integration. Syst. Biol., 60, 881-887.
9. Rodrigue, N. et al. (2010) Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. Proc. Natl Acad. Sci. USA., 107, 4629-4634.
10. Ronquist, F. and Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. (Pubitemid 37038874)