243 related articles for article (PubMed ID: 24927722)
1. 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. PubMed ID: 24927722
[TBL] [Abstract][Full Text] [Related]
2. 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; 8():331. PubMed ID: 19087270
[TBL] [Abstract][Full Text] [Related]
3. 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. PubMed ID: 25948563
[TBL] [Abstract][Full Text] [Related]
4. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.
Arenas M; Weber CC; Liberles DA; Bastolla U
Syst Biol; 2017 Nov; 66(6):1054-1064. PubMed ID: 28057858
[TBL] [Abstract][Full Text] [Related]
5. Phylogenetic inference with weighted codon evolutionary distances.
Criscuolo A; Michel CJ
J Mol Evol; 2009 Apr; 68(4):377-92. PubMed ID: 19308635
[TBL] [Abstract][Full Text] [Related]
6. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.
Shavit Grievink L; Penny D; Hendy MD; Holland BR
BMC Evol Biol; 2008 Nov; 8():317. PubMed ID: 19021917
[TBL] [Abstract][Full Text] [Related]
7. A model of evolution with constant selective pressure for regulatory DNA sites.
Enikeeva FN; Kotelnikova EA; Gelfand MS; Makeev VJ
BMC Evol Biol; 2007 Jul; 7():125. PubMed ID: 17662135
[TBL] [Abstract][Full Text] [Related]
8. Invariant Versus Classical Quartet Inference When Evolution is Heterogeneous Across Sites and Lineages.
Fernández-Sánchez J; Casanellas M
Syst Biol; 2016 Mar; 65(2):280-91. PubMed ID: 26559009
[TBL] [Abstract][Full Text] [Related]
9. Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly.
Ruano-Rubio V; Fares MA
Syst Biol; 2007 Feb; 56(1):68-82. PubMed ID: 17366138
[TBL] [Abstract][Full Text] [Related]
10. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
Miyazawa S
PLoS One; 2011; 6(12):e28892. PubMed ID: 22220197
[TBL] [Abstract][Full Text] [Related]
11. A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group.
Kawahara Y; Imanishi T
BMC Evol Biol; 2007 Jan; 7():9. PubMed ID: 17257443
[TBL] [Abstract][Full Text] [Related]
12. Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony.
Tourasse NJ; Gouy M
Mol Biol Evol; 1997 Mar; 14(3):287-98. PubMed ID: 9066796
[TBL] [Abstract][Full Text] [Related]
13. Position specific variation in the rate of evolution in transcription factor binding sites.
Moses AM; Chiang DY; Kellis M; Lander ES; Eisen MB
BMC Evol Biol; 2003 Aug; 3():19. PubMed ID: 12946282
[TBL] [Abstract][Full Text] [Related]
14. Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo.
Pagel M; Meade A
Philos Trans R Soc Lond B Biol Sci; 2008 Dec; 363(1512):3955-64. PubMed ID: 18852097
[TBL] [Abstract][Full Text] [Related]
15. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.
Buckley TR; Simon C; Chambers GK
Syst Biol; 2001 Feb; 50(1):67-86. PubMed ID: 12116595
[TBL] [Abstract][Full Text] [Related]
16. Empirical codon substitution matrix.
Schneider A; Cannarozzi GM; Gonnet GH
BMC Bioinformatics; 2005 Jun; 6():134. PubMed ID: 15927081
[TBL] [Abstract][Full Text] [Related]
17. Vestige: maximum likelihood phylogenetic footprinting.
Wakefield MJ; Maxwell P; Huttley GA
BMC Bioinformatics; 2005 May; 6():130. PubMed ID: 15921531
[TBL] [Abstract][Full Text] [Related]
18. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis.
Galtier N; Gouy M
Mol Biol Evol; 1998 Jul; 15(7):871-9. PubMed ID: 9656487
[TBL] [Abstract][Full Text] [Related]
19. Two stationary nonhomogeneous Markov models of nucleotide sequence evolution.
Jayaswal V; Jermiin LS; Poladian L; Robinson J
Syst Biol; 2011 Jan; 60(1):74-86. PubMed ID: 21081482
[TBL] [Abstract][Full Text] [Related]
20. A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.
Zhou Y; Brinkmann H; Rodrigue N; Lartillot N; Philippe H
Mol Biol Evol; 2010 Feb; 27(2):371-84. PubMed ID: 19822637
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
