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bioRxiv · 10.1101/487801

New methods to calculate concordance factors for phylogenomic datasets

Minh, B. Q.·Hahn, M.·Lanfear, R.
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Abstract

We implement two measures for quantifying genealogical concordance in phylogenomic datasets: 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).

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Minh, B. Q., Hahn, M., Lanfear, R.. 2018-12-05. New methods to calculate concordance factors for phylogenomic datasets. https://doi.org/10.1101/487801

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