ArticleNucleic acids research2016
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 556 papers, 1 of them a synthesis that pooled it.
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Who cites it
556 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review of mitochondrial genetic variation in attention-deficit/hyperactivity disorder.European child & adolescent psychiatry · 2024Pooled it
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- Genomic characterization of historical Jinlingnan individuals: insights into genetic continuity and trans-Eurasian signals in eastern China.Human genetics · 2026Article
- Genetic ancestry of the Mulam ethnic group: admixture from ancient Yellow River, southern native, and Austronesian populations.Human genetics · 2026Article
- Maternal lifetime stress and placental mitochondrial DNA mutational load: Effect modification by maternal characteristics.Placenta · 2026Article
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- Association of cord blood mitochondrial DNA heteroplasmy and copy number with childhood overweight or obesity.International journal of obesity (2005) · 2026Article
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- Ancient genomics study reveals low HLA diversity in eastern hunter-gatherers.Genome biology · 2026Article
- Genetic identification of Árpád Dynasty members from the ossuary of the Royal Basilica at Székesfehérvár.iScience · 2026Article
- Individual and joint association of maternal and cord blood mitochondrial DNA heteroplasmy and copy number with preterm birth.Pediatric research · 2026Article
- Equal in death: Ancient genomic analysis of children's early Christian burials.Science advances · 2026Article
- Genomic reconstruction of the Pakistani Roma reveals dual South Asian ancestry, medieval bottlenecks, and the early dispersal routes of the Romani people.Human genomics · 2026Article
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- Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.Science (New York, N.Y.) · 2026Article
- The genetic legacy of the 17th-century colonial capital of St. Mary's City.Current biology : CB · 2026Article
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- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
496 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at.
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