HaploGrouper: a generalized approach to haplogroup classification

Motivation: We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans. Results: HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species-given an extant annotated phylogenetic tree defined by sequence variants.

Automated summary

HaploGrouper is a versatile software that can classify haplotypes into haplogroups based on a known phylogenetic tree, providing flexibility and accuracy for assigning haplogroups to any type of haplotypes from any species.