The field of phylogenetics is entering a new era in which trees of historical relationships
between species are increasingly inferred from multilocus and genomic data. A major …

The unprecedented amount of data resulting from next-generation sequencing has opened
a new era in phylogenetic estimation. Although large datasets should, in theory, increase …

Until recently, it has been common practice for a phylogenetic analysis to use a single gene
sequence from a single individual organism as a proxy for an entire species. With …

The idea that all life on earth traces back to a common origin dates back at least to Charles
Darwin's Origin of Species. Ever since, biologists have tried to piece together parts of this …

Background Several phylogenetic approaches have been developed to estimate species
trees from collections of gene trees. However, maximum likelihood approaches for …

The advent and maturation of algorithms for estimating species trees—phylogenetic trees
that allow gene tree heterogeneity and whose tips represent lineages, populations and …

Species tree estimation is complicated by processes, such as gene duplication and loss and
incomplete lineage sorting (ILS), that cause discordance between gene trees and the …

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 …

The reconstruction of a species tree from genomic data faces a double hurdle. First, the
(gene) tree describing the evolution of each gene may differ from the species tree, for …

The estimation of species trees (phylogenies) is one of the most important problems in
evolutionary biology, and recently, there has been greater appreciation of the need to …