We implement two measures for quantifying genealogical concordance in phylogenomic
data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF) …

Topological conflict or incongruence is widespread in phylogenomic data. Concatenation-
and coalescent-based approaches often result in incongruent topologies, but the causes of …

Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant
discordances among phylogenies of different parts of genomes, as well as incongruences …

Background CADM is a statistical test used to estimate the level of Congruence Among
Distance Matrices. It has been shown in previous studies to have a correct rate of type I error …

Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The
method uses a non-parametric clustering of genes with compatible trees, and reconstructs …

Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Genome-level evolutionary inference (ie phylogenomics) is becoming an increasingly
essential step in many biologists' work. Accordingly, there are several tools available for the …

Reticulate evolution, whether due to lateral gene transfer, introgression, incomplete lineage
sorting, or hybrid speciation, is a ubiquitous phenomenon, yet systematists have few tools for …

Background Phylogenomic studies based on multi-locus sequence data sets are usually
characterized by partial taxon coverage, in which sequences for some loci are missing for …

Background While full genome sequences are still only available for a handful of taxa, large
collections of partial gene sequences are available for many more. The alignment of partial …