ASTER: A Package for Large-scale Phylogenomic Reconstructions.

Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-based species tree inference methods, collectively known as the ASTRAL family, are based on similar ideas and are in wide use. Here, we integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools, each designed for a different input type: (1) ASTRAL for single-copy gene tree topologies, (2) weighted ASTRAL (wASTRAL) for singlecopy gene tees with branch length and/or support, (3) ASTRAL-Pro for multi-copy gene tree topologies, (4) CASTER for multiple sequence alignments, including genome alignments, and (5)WASTER for shortreads and assembled genomes. These tools collectively enhance the scalability, accuracy, and versatility of species tree inference.