New Methods to Calculate Concordance Factors for Phylogenomic Datasets

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

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...