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Protocols specifications


Unique identifier OMICS_01643
Alternative name PhyloTreemt
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens


  • person_outline Mannis van Oven

Publication for citations


Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] plogroups were assigned with Haplogrep 2.0 ( Haplogroups showing a quality score below 100% were manually re-evaluated by consulting the established mtDNA phylogeny ( […]


The MT CO1 V83I Polymorphism is a Risk Factor for Primary Open Angle Glaucoma in African American Men

PMCID: 5886029
PMID: 29610859
DOI: 10.1167/iovs.17-23277

[…] Build 17 of PhyloTree (available in the public domain at and the MITOMAP and MITOMASTER databases (available in the public domain at were used to associate the observed mtDNA variants with mitochondrial haplogroups. The subce […]


Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

PLoS One
PMCID: 5844571
PMID: 29522562
DOI: 10.1371/journal.pone.0194223
call_split See protocol

[…] . SNPs were identified and haplogroups were assigned using Haplogrep 2.0 ( [] with the assistance of Mitomap ( [] and PhyloTree ( []. […]


Peculiar combinations of individually non pathogenic missense mitochondrial DNA variants cause low penetrance Leber’s hereditary optic neuropathy

PLoS Genet
PMCID: 5828459
PMID: 29444077
DOI: 10.1371/journal.pgen.1007210

[…] were recovered from two public databases, Mitomap ( and HmtDB ( [,]. Haplogroup affiliations of mitogenomes were assigned according to PhyloTree ( []. […]


A mosaic genetic structure of the human population living in the South Baltic region during the Iron Age

Sci Rep
PMCID: 5802798
PMID: 29410482
DOI: 10.1038/s41598-018-20705-6

[…] Haplogroups were predicted with HaploFind with respect to Phylotree build 17 ( Only samples with a haplogroup score ≥ 0.8 and average coverage ≥ 3 were used in downstream analyses. To assess temporal mtDNA haplogroup frequency changes from Mesolithic to the pres […]


Investigating the origins of eastern Polynesians using genome wide data from the Leeward Society Isles

Sci Rep
PMCID: 5789021
PMID: 29379068
DOI: 10.1038/s41598-018-20026-8
call_split See protocol

[…] The DNA extracts of 81 Leeward Society Islanders (Supplementary Table ) were genotyped for membership of mitochondrial haplogroups typical of eastern Polynesia–. Nomenclature followed that of, mtDNA tree Build 17 (Supplementary Table ). This resulted in 78 individuals allocated to the hg B4a1a1 and three individuals to hg Q. The control region (nps 57–372 and nps 16024–16526) […]


Looking to check out a full list of citations? institution(s)
Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, Netherlands funding source(s)
Supported by the Netherlands Forensic Institute. reviews

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