A Likelihood Framework to Measure Horizontal Gene Transfer

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dc.contributor.author Linz, Simone en
dc.contributor.author Radtke, A en
dc.contributor.author von Haeseler, A en
dc.date.accessioned 2015-02-01T22:30:56Z en
dc.date.issued 2007-03-10 en
dc.identifier.citation Molecular Biology and Evolution, 2007, 24 (6), pp. 1312 - 1319 en
dc.identifier.issn 0737-4038 en
dc.identifier.uri http://hdl.handle.net/2292/24347 en
dc.description.abstract We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees representing a set of taxa. As an illustrative example, we use the “Clusters of Orthologous Groups of proteins” (COGs). We also perform a correction of the estimated rate taking into account the inaccuracies due to gene tree reconstructions. The results suggest a corrected HGT rate of about 0.36 per gene and unit time, in other words 11 HGT events have occurred on average among the 44 taxa of the COG species tree. A software package to estimate an HGT rate is available online (http://www.cibiv.at/software/hgt/). en
dc.relation.ispartofseries Molecular Biology and Evolution en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. Details obtained from http://www.oxfordjournals.org/en/access-purchase/rights-and-permissions/self-archiving-policye.html http://www.sherpa.ac.uk/romeo/issn/0737-4038/ en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.title A Likelihood Framework to Measure Horizontal Gene Transfer en
dc.type Journal Article en
dc.identifier.doi 10.1093/molbev/msm052 en
pubs.issue 6 en
pubs.begin-page 1312 en
pubs.volume 24 en
dc.description.version AM - Accepted Manuscript en
pubs.end-page 1319 en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Article en
pubs.elements-id 460382 en
pubs.org-id Science en
pubs.org-id School of Computer Science en
dc.identifier.eissn 1537-1719 en
pubs.record-created-at-source-date 2015-02-02 en
pubs.dimensions-id 17374878 en

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