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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
call_split See protocol

[…] notation 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 except […]


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 are ac […]


The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes

Sci Rep
PMCID: 5278401
PMID: 28134350
DOI: 10.1038/srep41529

[…] mative as it is probable that the ends of the molecules were not read. No rescaling of base quality scores was applied.Mitochondrial haplogroups were also estimated for the three individuals () using Phy-Mer. For ethical reasons, the determined haplogroups are not reported in this paper; however, the two modern relatives, as expected, shared the same haplogroup, with a Phy-Mer confidence score of […]


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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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