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epiPALEOMIX specifications


Unique identifier OMICS_12830
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output data NucleoMap, MethylMap, Phasogram, WriteDepth
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Python, PySam
Maintained Yes




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  • person_outline Konstantin Krutovsky

Publication for epiPALEOMIX

epiPALEOMIX citation


Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX

Mol Biol Evol
PMCID: 5100044
PMID: 27624717
DOI: 10.1093/molbev/msw184

[…] been characterized, based, however, on a limited number of samples. the extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. here, we present epipaleomix, an open-source and user-friendly pipeline that exploits post-mortem dna degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment […]

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epiPALEOMIX institution(s)
Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, USA; Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, TX, USA; Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, Germany; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, Russia; USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, Saucier, MS, USA; University of Kentucky, Forest Health Research and Education Center, Lexington, KY, USA; Texas A&M Forest Service, College Station, TX, USA

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