A divide-and-conquer method for scalable phylogenetic network inference from multilocus data

dc.citation.firstpagei370en_US
dc.citation.issueNumber14en_US
dc.citation.journalTitleBioinformaticsen_US
dc.citation.lastpagei378en_US
dc.citation.volumeNumber35en_US
dc.contributor.authorZhu, Jiafanen_US
dc.contributor.authorLiu, Xinhaoen_US
dc.contributor.authorOgilvie, Huw A.en_US
dc.contributor.authorNakhleh, Luay K.en_US
dc.date.accessioned2019-08-28T16:10:11Zen_US
dc.date.available2019-08-28T16:10:11Zen_US
dc.date.issued2019en_US
dc.description.abstractMotivation: Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting. However, these methods can only handle a small number of loci from a handful of genomes. Results: In this article, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological datasets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with existing methods. The results are a significant and promising step towards accurate, large-scale phylogenetic network inference.en_US
dc.identifier.citationZhu, Jiafan, Liu, Xinhao, Ogilvie, Huw A., et al.. "A divide-and-conquer method for scalable phylogenetic network inference from multilocus data." <i>Bioinformatics,</i> 35, no. 14 (2019) Oxford University Press: i370-i378. https://doi.org/10.1093/bioinformatics/btz359.en_US
dc.identifier.doihttps://doi.org/10.1093/bioinformatics/btz359en_US
dc.identifier.urihttps://hdl.handle.net/1911/107367en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/en_US
dc.titleA divide-and-conquer method for scalable phylogenetic network inference from multilocus dataen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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