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dc.contributor.authorSchrempf, Dominik
dc.contributor.authorMinh, Bui Quang
dc.contributor.authorDe Maio, Nicola
dc.contributor.authorvon Haeseler, Arndt
dc.contributor.authorKosiol, Carolin
dc.date.accessioned2017-02-08T16:30:13Z
dc.date.available2017-02-08T16:30:13Z
dc.date.issued2016-10-21
dc.identifier249098317
dc.identifier94388175-4c44-4e35-999f-1e4c4110c90e
dc.identifier27480613
dc.identifier84982796242
dc.identifier.citationSchrempf , D , Minh , B Q , De Maio , N , von Haeseler , A & Kosiol , C 2016 , ' Reversible polymorphism-aware phylogenetic models and their application to tree inference ' , Journal of Theoretical Biology , vol. 407 , pp. 362-370 . https://doi.org/10.1016/j.jtbi.2016.07.042en
dc.identifier.issn0022-5193
dc.identifier.urihttps://hdl.handle.net/10023/10252
dc.descriptionThis work is supported by the Austrian Science Fund (FWF-P24551 and I-2805-B29) and partially by the Vienna Graduate School of Population Genetics (FWF-W1225).en
dc.description.abstractWe present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction.
dc.format.extent9
dc.format.extent769984
dc.language.isoeng
dc.relation.ispartofJournal of Theoretical Biologyen
dc.subjectSpecies treeen
dc.subjectPhylogeneticsen
dc.subjectIncomplete lineage sortingen
dc.subjectSubstitution modelen
dc.subjectReversible polymorphism-aware phylogenetic modelen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.subjectNDASen
dc.subjectBDCen
dc.subjectR2Cen
dc.subject.lccQH301en
dc.subject.lccQH426en
dc.titleReversible polymorphism-aware phylogenetic models and their application to tree inferenceen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.contributor.institutionUniversity of St Andrews. Centre for Biological Diversityen
dc.identifier.doi10.1016/j.jtbi.2016.07.042
dc.description.statusPeer revieweden


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