166 related articles for article (PubMed ID: 32068869)
1. Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.
Wisotsky SR; Kosakovsky Pond SL; Shank SD; Muse SV
Mol Biol Evol; 2020 Aug; 37(8):2430-2439. PubMed ID: 32068869
[TBL] [Abstract][Full Text] [Related]
2. Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.
Lucaci AG; Zehr JD; Enard D; Thornton JW; Kosakovsky Pond SL
Mol Biol Evol; 2023 Jul; 40(7):. PubMed ID: 37395787
[TBL] [Abstract][Full Text] [Related]
3. Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.
Davydov II; Salamin N; Robinson-Rechavi M
Mol Biol Evol; 2019 Jun; 36(6):1316-1332. PubMed ID: 30847475
[TBL] [Abstract][Full Text] [Related]
4. Not so different after all: a comparison of methods for detecting amino acid sites under selection.
Kosakovsky Pond SL; Frost SD
Mol Biol Evol; 2005 May; 22(5):1208-22. PubMed ID: 15703242
[TBL] [Abstract][Full Text] [Related]
5. Weak selection on synonymous codons substantially inflates
Rahman S; Kosakovsky Pond SL; Webb A; Hey J
Proc Natl Acad Sci U S A; 2021 May; 118(20):. PubMed ID: 33972434
[TBL] [Abstract][Full Text] [Related]
6. Gene-wide identification of episodic selection.
Murrell B; Weaver S; Smith MD; Wertheim JO; Murrell S; Aylward A; Eren K; Pollner T; Martin DP; Smith DM; Scheffler K; Kosakovsky Pond SL
Mol Biol Evol; 2015 May; 32(5):1365-71. PubMed ID: 25701167
[TBL] [Abstract][Full Text] [Related]
7. A random effects branch-site model for detecting episodic diversifying selection.
Kosakovsky Pond SL; Murrell B; Fourment M; Frost SD; Delport W; Scheffler K
Mol Biol Evol; 2011 Nov; 28(11):3033-43. PubMed ID: 21670087
[TBL] [Abstract][Full Text] [Related]
8. Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection.
Rubinstein ND; Doron-Faigenboim A; Mayrose I; Pupko T
Mol Biol Evol; 2011 Dec; 28(12):3297-308. PubMed ID: 21690564
[TBL] [Abstract][Full Text] [Related]
9. Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.
Dimitrieva S; Anisimova M
PLoS One; 2014; 9(6):e95034. PubMed ID: 24896293
[TBL] [Abstract][Full Text] [Related]
10. Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees.
Kusumi J; Tsumura Y; Yoshimaru H; Tachida H
Mol Biol Evol; 2002 May; 19(5):736-47. PubMed ID: 11961107
[TBL] [Abstract][Full Text] [Related]
11. The site-wise log-likelihood score is a good predictor of genes under positive selection.
Wang HC; Susko E; Roger AJ
J Mol Evol; 2013 May; 76(5):280-94. PubMed ID: 23595859
[TBL] [Abstract][Full Text] [Related]
12. Site-to-site variation of synonymous substitution rates.
Pond SK; Muse SV
Mol Biol Evol; 2005 Dec; 22(12):2375-85. PubMed ID: 16107593
[TBL] [Abstract][Full Text] [Related]
13. Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.
Rodrigue N; Lartillot N
Mol Biol Evol; 2017 Jan; 34(1):204-214. PubMed ID: 27744408
[TBL] [Abstract][Full Text] [Related]
14. The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.
Gharib WH; Robinson-Rechavi M
Mol Biol Evol; 2013 Jul; 30(7):1675-86. PubMed ID: 23558341
[TBL] [Abstract][Full Text] [Related]
15. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection.
Smith MD; Wertheim JO; Weaver S; Murrell B; Scheffler K; Kosakovsky Pond SL
Mol Biol Evol; 2015 May; 32(5):1342-53. PubMed ID: 25697341
[TBL] [Abstract][Full Text] [Related]
16. Multiple Factors Confounding Phylogenetic Detection of Selection on Codon Usage.
Laurin-Lemay S; Philippe H; Rodrigue N
Mol Biol Evol; 2018 Jun; 35(6):1463-1472. PubMed ID: 29596640
[TBL] [Abstract][Full Text] [Related]
17. Bayesian estimation of positively selected sites.
Huelsenbeck JP; Dyer KA
J Mol Evol; 2004 Jun; 58(6):661-72. PubMed ID: 15461423
[TBL] [Abstract][Full Text] [Related]
18. A Bayesian model comparison approach to inferring positive selection.
Scheffler K; Seoighe C
Mol Biol Evol; 2005 Dec; 22(12):2531-40. PubMed ID: 16120799
[TBL] [Abstract][Full Text] [Related]
19. Statistical properties of the branch-site test of positive selection.
Yang Z; dos Reis M
Mol Biol Evol; 2011 Mar; 28(3):1217-28. PubMed ID: 21087944
[TBL] [Abstract][Full Text] [Related]
20. Phylogenetic analysis and positive-selection site detecting of vascular endothelial growth factor family in vertebrates.
He W; Tang Y; Qi B; Lu C; Qin C; Wei Y; Yi J; Chen M
Gene; 2014 Feb; 535(2):345-52. PubMed ID: 24200960
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
