Human mtDNA Haplogroup
Track by Variant profiles
fragments/ full mtGenome
Conserved Region Map
for primer/ probe design
High-resolution haplogrouping with control/coding regions
High-resolution mtDNA haplogroup prediction using the Sanger sequencing of small fragmented control region sequences, tracking with coding region sequences for confirmation or sub-haplogrouping by narrowing and differentiating highly ranked haplogroups. DOI: 10.1101/2020.04.23.057646
High accuracy using control region sequences
Highly accurate prediction of haplogroup (HG) using control region (CR) or hypervariable 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 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 (most recent common ancestors).
- Proposes differential variants between HGs.
- Re-tracks with the fragments of proposed variants to confirm the HGs or to track sub-HGs.
- '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