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: (i) ASTRAL for single-copy gene tree topologies, (ii) weighted ASTRAL (wASTRAL) for single-copy gene tees with branch length and/or support, (iii) ASTRAL-Pro for multi-copy gene tree topologies, (iv) CASTER for multiple sequence alignments, including genome alignments, and (v) WASTER for short-reads and assembled genomes. These tools collectively enhance the scalability, accuracy, and versatility of species tree inference.