241 related articles for article (PubMed ID: 37576497)
1. 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]
2. 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]
3. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.
McCormack JE; Huang H; Knowles LL
Syst Biol; 2009 Oct; 58(5):501-8. PubMed ID: 20525604
[TBL] [Abstract][Full Text] [Related]
4. Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation.
Mar JC; Harlow TJ; Ragan MA
BMC Evol Biol; 2005 Jan; 5():8. PubMed ID: 15676079
[TBL] [Abstract][Full Text] [Related]
5. 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; 363(1512):4013-21. PubMed ID: 18852108
[TBL] [Abstract][Full Text] [Related]
6. nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.
Dang CC; Minh BQ; McShea H; Masel J; James JE; Vinh LS; Lanfear R
Syst Biol; 2022 Aug; 71(5):1110-1123. PubMed ID: 35139203
[TBL] [Abstract][Full Text] [Related]
7. The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.
Khurana MP; Scheidwasser-Clow N; Penn MJ; Bhatt S; Duchêne DA
Syst Biol; 2024 May; 73(1):235-246. PubMed ID: 38153910
[TBL] [Abstract][Full Text] [Related]
8. Estimating amino acid substitution models from genome datasets: a simulation study on the performance of estimated models.
Tinh NH; Dang CC; Vinh LS
J Evol Biol; 2024 Feb; 37(2):256-265. PubMed ID: 38366253
[TBL] [Abstract][Full Text] [Related]
9. The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae.
Ekman S; Blaalid R
Syst Biol; 2011 Jul; 60(4):541-61. PubMed ID: 21436107
[TBL] [Abstract][Full Text] [Related]
10. FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.
Dang CC; Le VS; Gascuel O; Hazes B; Le QS
BMC Bioinformatics; 2014 Oct; 15(1):341. PubMed ID: 25344302
[TBL] [Abstract][Full Text] [Related]
11. The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life.
Du Y; Wu S; Edwards SV; Liu L
BMC Evol Biol; 2019 Nov; 19(1):203. PubMed ID: 31694538
[TBL] [Abstract][Full Text] [Related]
12. The accuracy of species tree estimation under simulation: a comparison of methods.
Leaché AD; Rannala B
Syst Biol; 2011 Mar; 60(2):126-37. PubMed ID: 21088009
[TBL] [Abstract][Full Text] [Related]
13. Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study.
Vernygora OV; Simões TR; Campbell EO
Syst Biol; 2020 Nov; 69(6):1088-1105. PubMed ID: 32191335
[TBL] [Abstract][Full Text] [Related]
14. To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods.
Molloy EK; Warnow T
Syst Biol; 2018 Mar; 67(2):285-303. PubMed ID: 29029338
[TBL] [Abstract][Full Text] [Related]
15. Estimating species trees using approximate Bayesian computation.
Fan HH; Kubatko LS
Mol Phylogenet Evol; 2011 May; 59(2):354-63. PubMed ID: 21397706
[TBL] [Abstract][Full Text] [Related]
16. QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.
Minh BQ; Dang CC; Vinh LS; Lanfear R
Syst Biol; 2021 Aug; 70(5):1046-1060. PubMed ID: 33616668
[TBL] [Abstract][Full Text] [Related]
17. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.
De Oliveira Martins L; Mallo D; Posada D
Syst Biol; 2016 May; 65(3):397-416. PubMed ID: 25281847
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.
Liu K; Warnow TJ; Holder MT; Nelesen SM; Yu J; Stamatakis AP; Linder CR
Syst Biol; 2012 Jan; 61(1):90-106. PubMed ID: 22139466
[TBL] [Abstract][Full Text] [Related]
20. Bayesian coestimation of phylogeny and sequence alignment.
Lunter G; Miklós I; Drummond A; Jensen JL; Hein J
BMC Bioinformatics; 2005 Apr; 6():83. PubMed ID: 15804354
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]