This was part of
Contemporary Challenges in Large-Scale Sequence Alignments and Phylogenies
CASTLES-Pro
Yasamin Tabatabaee, University of Illinois at Urbana-Champaign
Thursday, August 14, 2025
Abstract: CASTLES-Pro (https://www.biorxiv.org/content/10.1101/2025.02.20.639320v1.abstract) is a method for estimating branch lengths of a species tree in substitution units from estimated gene trees accounting for both incomplete lineage sorting and gene duplication and loss. It is far more scalable than the traditional concatenation-based inference, easily scaling to datasets with tens of thousands of species and genes, and is more accurate than alternatives when gene tree discordance is at least moderate. CASTLES-Pro is implemented inside the ASTER software package available at https://github.com/chaoszhang/ASTER. In this demo, I will demonstrate how CASTLES-Pro can be used to estimate species tree branch lengths and how these lengths can be used for downstream tasks such as dating and diversification analysis.