Data from: Phylogenomic branch length estimation using quartets

Branch lengths and topology of a species tree are essential in most
downstream analyses, including estimation of diversification dates,
characterization of selection, understanding adaptation, and comparative
genomics. Modern phylogenomic analyses often use methods that account for
the heterogeneity of evolutionary histories across the genome due to
processes such as incomplete lineage sorting. However, these methods
typically do not generate branch lengths in units that are usable by
downstream applications, forcing phylogenomic analyses to resort to
alternative shortcuts such as estimating branch lengths by concatenating
gene alignments into a supermatrix. Yet, concatenation and other available
approaches for estimating branch lengths fail to address heterogeneity
across the genome. In this article, we derive expected values of gene tree
branch lengths in substitution units under an extension of the
multispecies coalescent (MSC) model that allows substitutions with varying
rates across the species tree. We present CASTLES, a new technique for
estimating branch lengths on the species tree from estimated gene trees
that uses these expected values, and our study shows that CASTLES improves
on the most accurate prior methods with respect to both speed and
accuracy.