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For: Squartini F, Arndt PF. Quantifying the stationarity and time reversibility of the nucleotide substitution process. Mol Biol Evol 2008;25:2525-35. [PMID: 18682605 DOI: 10.1093/molbev/msn169] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
Number Cited by Other Article(s)
1
Sianga-Mete R, Hartnady P, Mandikumba WC, Rutherford K, Currin CB, Phelanyane F, Stefan S, Kosakovsky Pond SL, Martin DP. Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models. RESEARCH SQUARE 2022:rs.3.rs-2407778. [PMID: 36597548 PMCID: PMC9810213 DOI: 10.21203/rs.3.rs-2407778/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
2
Dang CC, Minh BQ, McShea H, Masel J, James JE, Vinh LS, Lanfear R. OUP accepted manuscript. Syst Biol 2022;71:1110-1123. [PMID: 35139203 PMCID: PMC9366462 DOI: 10.1093/sysbio/syac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/30/2022] [Indexed: 11/12/2022]  Open
3
Naser-Khdour S, Minh BQ, Lanfear R. Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals. Syst Biol 2021;71:959-972. [PMID: 34387349 PMCID: PMC9260635 DOI: 10.1093/sysbio/syab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/14/2022]  Open
4
Hannaford NE, Heaps SE, Nye TMW, Williams TA, Embley TM. Incorporating compositional heterogeneity into Lie Markov models for phylogenetic inference. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
5
Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020;2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022]  Open
6
Zanin M, Rodríguez-González A, Menasalvas Ruiz E, Papo D. Assessing Time Series Reversibility through Permutation Patterns. ENTROPY (BASEL, SWITZERLAND) 2018;20:e20090665. [PMID: 33265754 PMCID: PMC7513188 DOI: 10.3390/e20090665] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
7
Cherlin S, Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM. The Effect of Nonreversibility on Inferring Rooted Phylogenies. Mol Biol Evol 2018;35:984-1002. [PMID: 29149300 PMCID: PMC5889004 DOI: 10.1093/molbev/msx294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
8
Kaehler BD. Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies. J Theor Biol 2017;420:144-151. [PMID: 28286217 DOI: 10.1016/j.jtbi.2017.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 10/20/2022]
9
Williams TA, Heaps SE, Cherlin S, Nye TMW, Boys RJ, Embley TM. New substitution models for rooting phylogenetic trees. Philos Trans R Soc Lond B Biol Sci 2015;370:20140336. [PMID: 26323766 PMCID: PMC4571574 DOI: 10.1098/rstb.2014.0336] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2015] [Indexed: 12/23/2022]  Open
10
De Maio N, Schlötterer C, Kosiol C. Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Mol Biol Evol 2013;30:2249-62. [PMID: 23906727 PMCID: PMC3773373 DOI: 10.1093/molbev/mst131] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
11
McCandlish DM. On the findability of genotypes. Evolution 2013;67:2592-603. [PMID: 24033169 DOI: 10.1111/evo.12128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 03/14/2013] [Indexed: 02/02/2023]
12
Altenberg L. The evolution of dispersal in random environments and the principle of partial control. ECOL MONOGR 2012. [DOI: 10.1890/11-1136.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
13
An Evolutionary Reduction Principle for Mutation Rates at Multiple Loci. Bull Math Biol 2010;73:1227-70. [DOI: 10.1007/s11538-010-9557-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 06/04/2010] [Indexed: 01/07/2023]
14
Polak P, Arndt PF. Long-range bidirectional strand asymmetries originate at CpG islands in the human genome. Genome Biol Evol 2009;1:189-97. [PMID: 20333189 PMCID: PMC2817419 DOI: 10.1093/gbe/evp024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2009] [Indexed: 12/24/2022]  Open
15
Schneider A, Cannarozzi GM. Support patterns from different outgroups provide a strong phylogenetic signal. Mol Biol Evol 2009;26:1259-72. [PMID: 19240194 DOI: 10.1093/molbev/msp034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
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