Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss

Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to incomplete lineage sorting. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch l..., , ## CASTLES-Pro Datasets

This repository contains the datasets and scripts used in the following paper:

* Y. Tabatabaee, C. Zhang, S. Arasti, S. Mirarab (2025). Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss. Genome Biology and Evolution. Volume 17, Issue 11. [https://academic.oup.com/gbe/article/17/11/evaf200/8343050](https://academic.oup.com/gbe/article/17/11/evaf200/8343050)

For experiments in this study, we analyzed three sets of simulated datasets and nine biological datasets with different sources of gene tree discordance. In all simulated datasets, the true species trees have branch lengths in substitution-units.

We provide a description of the relevant files included in each dataset below. Note that some log and intermediate files generated during the analyses are also included with the datasets for completeness, but are not listed here.

### Simulated datasets

**ILS-only simulations**

For the ILS simulations, we reused the 1...,