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dc.contributor.authorSchrempf, Dominik
dc.contributor.authorMinh, Bui Quang
dc.contributor.authorvon Haeseler, Arndt
dc.contributor.authorKosiol, Carolin
dc.identifier.citationSchrempf , D , Minh , B Q , von Haeseler , A & Kosiol , C 2019 , ' Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity ' , Molecular Biology and Evolution , vol. 36 , no. 6 , pp. 1294-1301 .
dc.identifier.otherPURE: 258073629
dc.identifier.otherPURE UUID: 95ada2a4-9426-4292-8d30-1424e160c3bb
dc.identifier.otherScopus: 85066425176
dc.identifier.otherWOS: 000473587400015
dc.descriptionThis work was funded by the Vienna Science and Technology Fund (WWTF) through project MA16-061. DS was supported by the Austrian Science Fund [FWF-P24551, I-2805-B29] and received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 741774. The computational results presented have been achieved in part using the Vienna Scientific Cluster (VSC) and the St Andrews Bioinformatics Unit (StABU) which is funded by a Wellcome Trust ISSF award (grant 105621/Z/14/Z). BQM was supported by the Australian National University Futures grant.en
dc.description.abstractMolecular phylogenetics has neglected polymorphisms within present and ancestral populations for a long time. Recently, multispecies coalescent based methods have increased in popularity, however, their application is limited to a small number of species and individuals. We introduced a polymorphism-aware phylogenetic model (PoMo), which overcomes this limitation and scales well with the increasing amount of sequence data while accounting for present and ancestral polymorphisms. PoMo circumvents handling of gene trees and directly infers species trees from allele frequency data. Here, we extend the PoMo implementation in IQ-TREE and integrate search for the statistically best-fit mutation model, the ability to infer mutation rate variation across sites, and assessment of branch support values. We exemplify an analysis of a hundred species with ten haploid individuals each, showing that PoMo can perform inference on large data sets. While PoMo is more accurate than standard substitution models applied to concatenated alignments, it is almost as fast. We also provide bmm-simulate, a software package that allows simulation of sequences evolving under PoMo. The new options consolidate the value of PoMo for phylogenetic analyses with population data.
dc.relation.ispartofMolecular Biology and Evolutionen
dc.rightsCopyright © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectIncomplete lineage sortingen
dc.subjectSpecies treeen
dc.subjectPhylogenetic modelen
dc.subjectBoundary mutation modelen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.titlePolymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneityen
dc.typeJournal articleen
dc.contributor.sponsorThe Wellcome Trusten
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. Centre for Biological Diversityen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.description.statusPeer revieweden

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