New Methods to Calculate Concordance Factors for Phylogenomic Datasets.

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).