Multi-method gene clusters at species-level resolution for 125 prokaryotic pangenomes

This dataset contains 9 sets of species-level gene clusters and high-resolution species trees for 125 representative bacterial and archaeal species, encompassing a total of 6,851 nearly complete genomes. Each set represents a different approach to homology, orthology, and synteny-based gene clustering as implemented by 6 popular tools for comparative genomics and pangenome analysis (Roary, panX, OrthoFinder, MMseqs2/PanACoTa, CD-HIT, and eggNOG-mapper). This dataset is a helpful resource for benchmarking gene clustering tools and pangenome analysis workflows.