ArticleNucleic acids research2023
Haplogrep 3 - an interactive haplogroup classification and analysis platform.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- Initial Genome-Wide Characterization of Turkmen Individuals from the Dashoguz Region, Turkmenistan.Biology · 2026Article
- Genetic ancestry and monogenic disease risk in the Scottish Traveller founder population.Nature communications · 2026Article
- Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar Desert.HGG advances · 2026Article
- DNA signatures preserved in the official 1978 sample collection of the Shroud of Turin.Scientific reports · 2026Article
- Ancient DNA reveals elite dynastic rule among Iron Age Eurasian Steppe nomads.Science advances · 2026Article
- Metagenomic peek into a corn mummy.Scientific reports · 2026Article
- The genetic landscape of northeastern Iberian communities from the early to late Iron Age.iScience · 2026Article
- Large-scale mitogenome analysis reveals complex maternal genetic connections between Sino-Tibetan- and Altaic-speaking populations.Human genetics · 2026Article
- Revisiting the African mtDNA landscape through complete mitochondrial genomes.Communications biology · 2026Article
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- Contrasting ancestry patterns inferred from Y chromosome and mitochondrial DNA in Nanjing people from southwestern China.Human genetics · 2026Article
- Demographic History of Indigenous Populations in Mexico Explored Through Whole Mitogenome Analysis.Genome biology and evolution · 2026Article
- Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences.bioRxiv : the preprint server for biology · 2026Article
- An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.Nature communications · 2026Article
- Genetic genealogy of the Piast dynasty and related European royal families.Nature communications · 2026Article
- Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last decade, Haplogrep has become a standard tool for haplogroup classification in the field of human mitochondrial DNA and is widely used by medical, forensic, and evolutionary researchers. Haplogrep scales well for thousands of samples, supports many file formats and provides an intuitive graphical web interface. Nevertheless, the currently available version has limitations when applying it to large biobank-scale data. In this paper, we present a major upgrade to the software by adding (a) haplogroup summary statistics and variant annotations from various publicly available genome databases, (b) an interface to connect new phylogenetic trees, (c) a new state-of-the-art web framework managing large scale data, (d) algorithmic adaptions to improve FASTA classification using BWA-specific alignment rules and (e) a pre-classification quality control step for VCF samples. These improvements will give researchers the opportunity to classify thousands of samples as usual but providing additional ways to investigate the dataset directly in the browser. The web service and its documentation can be accessed freely without any registration at https://haplogrep.i-med.ac.at.
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