OMAmer

Tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. OMAmer is a novel alignment-free protein family assignment method, which limits over-specific subfamily assignments and is suited to phylogenomic databases with thousands of genomes. It is based on an innovative method using subfamily-informed k-mers for alignment-free mapping to ancestral protein subfamilies. Whilst able to reject non-homologous family-level assignments, it has provided better and quicker subfamily-level assignments than a method based on closest sequences (using DIAMOND).