High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

Species tree estimation is a basic part of many biological research projects, ranging from
answering basic evolutionary questions (eg, how did a group of species adapt to their …

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder's
high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted …

Background Evolutionary histories can be discordant across the genome, and such
discordances need to be considered in reconstructing the species phylogeny. ASTRAL is …

Although reconstruction of the phylogeny of living birds has progressed tremendously in the
last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living …

Species tree reconstruction is complicated by effects of incomplete lineage sorting,
commonly modeled by the multi-species coalescent model (MSC). While there has been …

Summary Butterflies (Papilionoidea), with over 18,000 described species [1], have
captivated naturalists and scientists for centuries. They play a central role in the study of …

Motivation: The estimation of species phylogenies requires multiple loci, since different loci
can have different trees due to incomplete lineage sorting, modeled by the multi-species …

Species tree inference is fundamental to our understanding of the evolution of life on earth.
However, species tree inference from molecular sequence data is complicated by gene …

The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of
data collection that leverage both genomic resources and recent advances in DNA …