About HaploGrep

HaploGrep provides a fully automated way to determine the haplogroup of mtDNA profiles. It supports standardized input (e.g. VCF) and output (e.g. VCF, fasta, multiple alignment) formats and provides several tools for an intensive quality control. So far (February 2016) HaploGrep has been cited over 175 times.

HaploGrep is implemented as a web application based on Phylotree, a periodically updated classification tree estimated from data worldwide. Any given range of the mitochondrial genome can be used for haplogroup classification, which is based on the phylogenetic stability of mtDNA polymorphisms. For every input sample the top ten results and the phylogenetic position of the respective haplogroup are displayed, thus providing a detailed explanation how and why a haplogroup was ranked best. HaploGrep generates an interactive data visualization of the results and provides recommendations which polymorphisms should be analyzed additionally to get a more accurate result. HaploGrep is free and can be used without any login.

HaploGrep Publications:

Weissensteiner H., Pacher D., Kloss-Brandstätter A., Forer L., Specht G., Bandelt H.-J., Kronenberg F., Salas A., Schönherr S. 2016. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucl. Acids. Res. 2016 Apr 15; doi:10.1093/nar/gkw233

Kloss-Brandstätter A., Pacher D., Schönherr S., Weissensteiner H., Binna R., Specht G., Kronenberg F. 2011. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups Hum Mutat. 2011 Jan;32(1):25-32. doi: 10.1002/humu.21382. Epub 2010 Nov 16.

Please cite us together with Phylotree:

van Oven M. 2015 PhyloTree Build 17: Growing the human mitochondrial DNA tree. Forensic Science International: Genetics Supplement Series 5: 9-11. http://linkinghub.elsevier.com/retrieve/pii/S1875176815302432. doi:10.1016/j.fsigss.2015.09.155. or van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.phylotree.org . doi:10.1002/humu.20921