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 acros..., , # Data from: Phylogenomic branch length estimation using quartets

This repository contains the datasets used in the following paper:

Y. Tabatabaee, C. Zhang, T. Warnow, S. Mirarab, Phylogenomic branch length estimation using quartets, Bioinformatics, Volume 39, Issue Supplement_1, June 2023, Pages i185–i193, [https://doi.org/10.1093/bioinformatics/btad221](https://doi.org/10.1093/bioinformatics/btad221)

For experiments in this study, we studied a collection of simulated and biological datasets with incomplete lineage sorting (ILS). We generated a new quartet dataset and regenerated species trees with substitution-unit branch lengths for previously published datasets from [Zhang et. al. (2018)](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2129-y) and [Mai et. al. (2017)](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182238). We also analyzed the mammalian biological dataset from [Song et. al. (2012)](https://www.pnas.org/doi/full/10.1073...,