Minh, Bui QuangHahn, Matthew W.Lanfear, Robert2021-02-212021-02-210737-4038http://hdl.handle.net/1885/223648We 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).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.).application/pdfen-AU© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolutionhttp://creativecommons.org/ licenses/by/4.0/phylogenetic inferenceconcordance factorphylogenomics202010.1093/molbev/msaa1062020-11-08Creative Commons Attribution License