219 related articles for article (PubMed ID: 38374231)
1. Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.
Ferreiro D; Branco C; Arenas M
Bioinformatics; 2024 Mar; 40(3):. PubMed ID: 38374231
[TBL] [Abstract][Full Text] [Related]
2. ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.
Arenas M
Bioinformatics; 2021 Dec; 38(1):58-64. PubMed ID: 34450622
[TBL] [Abstract][Full Text] [Related]
3. CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.
Arenas M; Lopes JS; Beaumont MA; Posada D
Mol Biol Evol; 2015 Apr; 32(4):1109-12. PubMed ID: 25577191
[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. Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies.
Laurin-Lemay S; Dickson K; Rodrigue N
J Mol Evol; 2022 Aug; 90(3-4):239-243. PubMed ID: 35652926
[TBL] [Abstract][Full Text] [Related]
6. Substitution Models of Protein Evolution with Selection on Enzymatic Activity.
Ferreiro D; Khalil R; Sousa SF; Arenas M
Mol Biol Evol; 2024 Feb; 41(2):. PubMed ID: 38314876
[TBL] [Abstract][Full Text] [Related]
7. GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation.
Tankhilevich E; Ish-Horowicz J; Hameed T; Roesch E; Kleijn I; Stumpf MPH; He F
Bioinformatics; 2020 May; 36(10):3286-3287. PubMed ID: 32022854
[TBL] [Abstract][Full Text] [Related]
8. Assessment of substitution model adequacy using frequentist and Bayesian methods.
Ripplinger J; Sullivan J
Mol Biol Evol; 2010 Dec; 27(12):2790-803. PubMed ID: 20616145
[TBL] [Abstract][Full Text] [Related]
9. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference.
Bastolla U; Arenas M
Methods Mol Biol; 2019; 1851():215-231. PubMed ID: 30298399
[TBL] [Abstract][Full Text] [Related]
10. Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.
Lopes JS; Arenas M; Posada D; Beaumont MA
Heredity (Edinb); 2014 Mar; 112(3):255-64. PubMed ID: 24149652
[TBL] [Abstract][Full Text] [Related]
11. Data-specific substitution models improve protein-based phylogenetics.
Brazão JM; Foster PG; Cox CJ
PeerJ; 2023; 11():e15716. PubMed ID: 37576497
[TBL] [Abstract][Full Text] [Related]
12. Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models.
Laurin-Lemay S; Rodrigue N; Lartillot N; Philippe H
Mol Biol Evol; 2018 Nov; 35(11):2819-2834. PubMed ID: 30203003
[TBL] [Abstract][Full Text] [Related]
13. Protein evolution along phylogenetic histories under structurally constrained substitution models.
Arenas M; Dos Santos HG; Posada D; Bastolla U
Bioinformatics; 2013 Dec; 29(23):3020-8. PubMed ID: 24037213
[TBL] [Abstract][Full Text] [Related]
14. 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; 14():85. PubMed ID: 23497171
[TBL] [Abstract][Full Text] [Related]
15. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models.
Del Amparo R; Arenas M
Genes (Basel); 2021 Dec; 13(1):. PubMed ID: 35052404
[TBL] [Abstract][Full Text] [Related]
16. Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.
Arenas M; Sánchez-Cobos A; Bastolla U
Mol Biol Evol; 2015 Aug; 32(8):2195-207. PubMed ID: 25837579
[TBL] [Abstract][Full Text] [Related]
17. Cross-validation to select Bayesian hierarchical models in phylogenetics.
Duchêne S; Duchêne DA; Di Giallonardo F; Eden JS; Geoghegan JL; Holt KE; Ho SY; Holmes EC
BMC Evol Biol; 2016 May; 16(1):115. PubMed ID: 27230264
[TBL] [Abstract][Full Text] [Related]
18. Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint.
Spielman SJ; Wilke CO
Mol Biol Evol; 2016 Nov; 33(11):2990-3002. PubMed ID: 27512115
[TBL] [Abstract][Full Text] [Related]
19. Influence of substitution model selection on protein phylogenetic tree reconstruction.
Del Amparo R; Arenas M
Gene; 2023 May; 865():147336. PubMed ID: 36871672
[TBL] [Abstract][Full Text] [Related]
20. 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. PubMed ID: 24441033
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
