Journal
BIOINFORMATICS
Volume 37, Issue 4, Pages 570-572Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa729
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Funding
- EUROTAST Marie Curie Framework Programme 7 Initial Training Network [290344]
- University of Iceland
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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.
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.
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