PMDtools statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PMDtools

Tool usage distribution map

This map represents all the scientific publications referring to PMDtools per scientific context
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PMDtools specifications


Unique identifier OMICS_08848
Name PMDtools
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data PMDtools takes SAM-formatted input, and requires an MD tag with alignment information.
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.50
Stability Stable
Maintained Yes


No version available



  • person_outline Pontus Skoglund

Publication for PMDtools

PMDtools citations


Biological Sexing of a 4000 Year Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] he calculation, RX and RY were also determined using only reads showing signs of damage, as these reads are unlikely to have originated from modern contaminants []. Read filtering was performed using PMDtools (v0.50; []) with a threshold of three, as recommended by the author of the program. […]


A female Viking warrior confirmed by genomics

PMCID: 5724682
PMID: 28884802
DOI: 10.1002/ajpa.23308

[…] ragments were then checked for presence of 3′ and 5′ degradation patterns characteristic of ancient DNA (Briggs et al., , Brotherton et al., , Sawyer, Krause, Guschanski, Savolainen, & Pääbo, ) using PMDtools (Skoglund et al., ). Molecular sex assignment was estimated based on the ratio of sequences aligning to the two sex chromosomes, X and Y (Skoglund, Storå, Götherström, & Jakobsson, ) (Figure […]


A new model for ancient DNA decay based on paleogenomic meta analysis

Nucleic Acids Res
PMCID: 5499742
PMID: 28486705
DOI: 10.1093/nar/gkx361

[…] en generated using a proofreading Platinum High Fidelity Taq polymerase (). We mapped all Saqqaq read files from the Sequence Read Archive (n = 218) to a human mitochondrial genome (EU256375.1), used PMDtools () to rapidly generate misincorporation plots and visually inspected each for elevated 5΄ C-to-T mismatch. This approach yielded two libraries apparently produced using a proofreading enzyme, […]


Archaeogenomic evidence reveals prehistoric matrilineal dynasty

Nat Commun
PMCID: 5321759
PMID: 28221340
DOI: 10.1038/ncomms14115

[…] ause of misalignment and were manually corrected based on visualization of the sequence reads.To verify support for the consensus haplotype among only reads with deaminated cytosine residues, we used PMDtools to generate BAM files from fragments having a minimum post-mortem degradation (PMD) score of 3, retaining ∼15–43% of reads per alignment. We re-ran mapDamage to generate new lambda values, ma […]


Improving ancient DNA genome assembly

PMCID: 5384568
PMID: 28392981
DOI: 10.7717/peerj.3126

[…] nst a reference genome allows researchers to easily eliminate non-endogenous DNA and identify erroneous base incorporations. These errors can be identified after the mapping, e.g., by mapDamage () or PMDtools (), and used to verify that the sequenced fragments stem from ancient specimen.The reference-based mapping approaches cannot detect large insertions or other genomic architectural rearrangeme […]


Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Nat Commun
PMCID: 5095515
PMID: 27796282
DOI: 10.1038/ncomms13195

[…] thout further fragmentation. To assess the potential contribution of post mortem DNA damage which could confound the population genetic analyses, we quantified cytosine deamination at read ends using PMDTools. Visual inspection of the frequency distribution of PMD scores did not reflect any differences between museum specimens and freshly collected samples, suggesting no substantial post mortem DN […]

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PMDtools institution(s)
Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences Siberian Branch, Novosibirsk, Russia; Institute for Archaeological Sciences, University of Tuebingen, Tuebingen, Germany

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