Human mtDNA Haplogroup

Track by Sequence

fragments/ full mtGenome

Track by Variant profiles

fragments/ full mtGenome

Conserved Region Map

for primer/ probe design


"High-resolution haplogroup classification tool designed for ancient DNA samples"

An mtDNA haplogrouping application specifically designed for ancient DNA or severely degraded DNA samples: High-resolution mtDNA haplogroup prediction using small fragmented control region (CR) sequences, straightforward tracking for confirmation or sub-haplogrouping by narrowing and differentiating highly ranked haplogroups, and conserved region mapping for successful primer design.
DOI: 10.1101/2020.04.23.057646

High Accuracy using Control-region sequences

Highly accurate prediction of HG using CR or HV region sequence fragments.

  • Using a novel algorithm based on PhyloTree definitions and our scoring system built with big data of haplotypes (n=118,869)
  • Extensively evaluated with 54,538 CR sequence samples comparing with HaploGrep 2.

A novel HG-tracking solution

It was established through repeated blind simulation tests

  • Inputs sequence fragments via a unique user-friendly interface
  • Minimizes the number of tests for HG tracking by narrowing down the predicted HGs by the integration of HGs to their MRCAs
  • Proposes differential variants between HGs
  • Re-tracks with the fragments of proposed variants to confirm the HGs or to track sub-haplogroups

Additional tools

  • 'HG tracking by fragment variant profiles' for variant profile input instead of sequences once the sample fragments are sequenced and their variants are extracted using the main tool.
  • 'Conserved region mapping tool for primer design' to secure successful PCR that is necessary to obtain additional sequences for further tracking.
  • 'HG database' to explore Phylotree HGs and their sub-haplogroups with their defining variant profiles.
  • 'Differntiation between HGs' to find differential variant information among user-inputted HGs.
  • QC tools: analysis of potential artificial recombination (included in main tools) and potential phantom mutants in a dataset
  • Variant format conversion tool for Phlyotreee, MitoTool, HaploGrep 2, and EMPOP
  • Major HG-specific variants

Super-HG prediction rates with CR sequences

Super-HG prediction rates