A simple python module to process output from MapQTL analysis.
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Latest commit 6d84dea Jul 1, 2013 @pypingou pypingou Release v1.1.0
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Author: Pierre-Yves Chibon <pierre-yves.chibon@wur.nl>, <pingou@pingoured.fr>

A simple python module to process output from QTL mapping tool including MapQTL and R/qtl.

Assuming one QTL per linkage group and using the LOD threshold set by the user. This application extracts all the QTLs detected by the QTL mapping tool, it finds the closest marker and finally put the number of QTLs found for each marker on the genetic map.

This approach quickly allows you to find potential QTL hotspot in your dataset. This is particularly usefull for large QTL analysis on a large number of traits.

Get this project:

Sources: https://github.com/PBR/MQ2

Release: http://pypi.python.org/packages/source/M/MQ2/MQ2-1.0.0.tar.gz

Run it on the web at: http://www.plantbreeding.nl/mq2


  • straight.plugin
  • xlrd (only required by the Excel plugin, if not present only this plugin will be affected)


The project contains some documentation on how to install, run and contribute to this project.

The documentation can be found: - online at: https://github.com/PBR/MQ2/tree/master/doc - as pdf at: https://github.com/PBR/MQ2/tree/master/MQ2_doc.pdf?raw=true

Run the project:

To run the project, simply run the MQ2 script provided.

See MQ2 --help or MQ2 -h for the different argument available.


This project contains unit-tests allowing you to check if the code behaves as it should.

To run them, two ways, either:



python setup.py nosetest


You will need to have python-coverage installed to run the test via runtest.sh


This project is licensed GPLv3+.