New Methods to Calculate Concordance Factors for Phylogenomic Datasets
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Minh, Bui Quang; Hahn, Matthew W.; Lanfear, Robert
Description
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of...[Show more]
dc.contributor.author | Minh, Bui Quang | |
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dc.contributor.author | Hahn, Matthew W. | |
dc.contributor.author | Lanfear, Robert | |
dc.date.accessioned | 2021-02-21T22:36:05Z | |
dc.date.available | 2021-02-21T22:36:05Z | |
dc.identifier.issn | 0737-4038 | |
dc.identifier.uri | http://hdl.handle.net/1885/223648 | |
dc.description.abstract | We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/ Concordance-Factor, last accessed May 13, 2020). | |
dc.description.sponsorship | This work was supported by National Science Foundation (Grant No. DEB-1936187 to M.W.H.), an Australian National University Futures Grant (to R.L.), and an Australian Research Council (Grant No. DP200103151 to R.L., B.Q.M., and M.W.H.). | |
dc.format.mimetype | application/pdf | |
dc.language.iso | en_AU | |
dc.publisher | Society for Molecular Biology Evolution | |
dc.rights | © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution | |
dc.rights.uri | http://creativecommons.org/ licenses/by/4.0/ | |
dc.source | Molecular Biology and Evolution | |
dc.subject | phylogenetic inference | |
dc.subject | concordance factor | |
dc.subject | phylogenomics | |
dc.title | New Methods to Calculate Concordance Factors for Phylogenomic Datasets | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 37 | |
dc.date.issued | 2020 | |
local.identifier.absfor | 060102 - Bioinformatics | |
local.identifier.absfor | 060409 - Molecular Evolution | |
local.identifier.absfor | 010402 - Biostatistics | |
local.identifier.ariespublication | u9511635xPUB2058 | |
local.publisher.url | http://mbe.oxfordjournals.org/ | |
local.type.status | Published Version | |
local.contributor.affiliation | Bui, Minh, College of Science, ANU | |
local.contributor.affiliation | Hahn, Matthew W., Indiana University | |
local.contributor.affiliation | Lanfear, Robert, College of Science, ANU | |
local.bibliographicCitation.issue | 9 | |
local.bibliographicCitation.startpage | 2727 | |
local.bibliographicCitation.lastpage | 2733 | |
local.identifier.doi | 10.1093/molbev/msaa106 | |
local.identifier.absseo | 970108 - Expanding Knowledge in the Information and Computing Sciences | |
local.identifier.absseo | 970106 - Expanding Knowledge in the Biological Sciences | |
dc.date.updated | 2020-11-08T07:25:32Z | |
dcterms.accessRights | Open Access | |
dc.provenance | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | |
dc.rights.license | Creative Commons Attribution License | |
Collections | ANU Research Publications |
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