Haplogrep 3 is a fast and free haplogroup classification tool
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Haplogrep 3 is a fast and free haplogroup classification tool. Upload your mtDNA profiles in FASTA, VCF or txt-based format and receive mitochondrial haplogroups, summary statistics and variant annotations in return. We provide Haplogrep 3 as a graphical web service or as a command-line tool for local usage. (copied from haplogrep3 docs)
All of the default trees of Haplogrep are installed in the docker image. These trees are described in the docs as follows.
Haplogrep currently supports different mitochonddrial (mtDNA) phylogenies (e.g. Phylotree 15 - 17, Phylotree Forensic Update) which are provided for different references (rCRS and RSRS). A list of available trees is available here. For reproducibility, each tree is hosted in its on repository (e.g. Phylotree 17).
./haplogrep3 classify --tree <tree-id> --input <input-file> --output <output-file>
Schönherr S, Weissensteiner H, Kronenberg F, Forer L. Haplogrep 3 - an interactive haplogroup classification and analysis platform. Nucleic Acids Res. 2023. https://doi.org/10.1093/nar/gkad284
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Image
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sha256:7b28d98a0…
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417.6 MB
Last updated
over 1 year ago
docker pull jtb114/haplogrep3