RT Journal Article
SR Electronic
T1 New methods to calculate concordance factors for phylogenomic datasets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 487801
DO 10.1101/487801
A1 Bui Quang Minh
A1 Matthew W. Hahn
A1 Robert Lanfear
YR 2018
UL http://biorxiv.org/content/early/2018/12/05/487801.abstract
AB Summary We introduce and implement two measures for quantifying genealogical concordance in phylogenomic datasets: the gene concordance factor (gCF) and the 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.Availability and Implementation An easy to use implementation and tutorial is freely available in the IQ-TREE software (http://www.iqtree.org).Supplementary information Data are available at https://doi.org/10.5281/zenodo.1949290Issue Section PhylogeneticsContact m.bui{at}anu.edu.au