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Phy-Mer specifications


Unique identifier OMICS_07992
Name Phy-Mer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU Affero General Public License version 3
Computer skills Advanced
Stability Stable
Python, PySam, BioPython
Maintained Yes


  • Primates
    • Homo sapiens


No version available



  • person_outline Xiaowu Gai

Publication for Phy-Mer

Phy-Mer citations


Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping

PMCID: 5961720
PMID: 29306584
DOI: 10.1016/j.jalz.2017.11.013

[…] information to the header lines. for each variant that was reported by multiple studies in mitomap, we included all studies in the annotation., next, we annotated mitochondrial haplotypes with phy-mer []. phy-mer reports the five most likely mitochondrial haplotypes and a score, where 1 is a perfect score. for each of the samples, we selected the top hit. all samples had scores >0.99 […]


Clinical utility of the low density Infinium QC genotyping Array in a genomics based diagnostics laboratory

BMC Med Genomics
PMCID: 5639583
PMID: 28985730
DOI: 10.1186/s12920-017-0297-7

[…] clinical exome sequencing (ces) data. we ran haplogrep 2 ( [] on the infinium qc data and compared the respective haplogroup assignments with the haplogroup calls made by phy-mer ( [] using the ces data of very high-depth of mitochondrial genome coverage. phy-mer haplogroup calls made upon entire mtdna sequence […]

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Phy-Mer institution(s)
Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA

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