mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.
bin The --mapdamage-modules option can now be specified with an equal sign Feb 19, 2015
mapdamage Add explicit check for empty FASTA/fai files. Jul 30, 2018
.gitignore Updated the ignore file to incorporate various temporary files Sep 3, 2013
MANIFEST python version first commit Nov 12, 2012 add reading a BAM from stdin Nov 14, 2012 update README Aug 2, 2016 Improve tag handling. Apr 27, 2017


Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of mapDamage to use half of the data for estimation of the damage parameters, sorry for the inconvenience.


Complete documentation, instructions, examples, screenshots and FAQ are available at this address.

mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

Mapdamage is developed at the Centre for GeoGenetics by the Orlando Group .

Web interface

Anna Kostikova from insideDNA implemented a web interface for mapDamage.
Users can adjust the cloud ressources in terms of RAM/CPU to perform their analysis. She wrote a tutorial explaining how to use this web interface (sign up required)


If you use this program, please cite the following publication:
Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 23rd April 2013. doi: 10.1093/bioinformatics/btt193

The original mapDamage1 is described in the following article:
Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 2011 27(15):2153-5


Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email: aginolhac at, MSchubert at or jonsson.hakon at