New Methods to Calculate Concordance Factors for Phylogenomic Datasets

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 me...

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Published inMolecular biology and evolution Vol. 37; no. 9; pp. 2727 - 2733
Main Authors Minh, Bui Quang, Hahn, Matthew W, Lanfear, Robert
Format Journal Article
LanguageEnglish
Published United States Oxford University Press 01.09.2020
Subjects
Datasets as Topic
Genetic Techniques
Methods
Phylogeny
Software
Trees
concordance factor
phylogenetic inference
phylogenomics
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Summary: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).
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ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/msaa106