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QTL Cartographer

is a suite of programs to map quantitative traits using a map of molecular markers. The programs are available via an anonymous ftp server. See the README for more information. You will also want a copy of Gnuplot to display plots made by QTL Cartographer. Gnuplot is freely available on the web. Do a search to find the latest version for your operating system.

Windows QTL Cartographer

Windows QTL Cartographer is a user friendly version of QTL Cartographer. It has a GUI interface and runs under Microsoft Windows.


The manual for QTL Cartographer is written in LaTeX2e. An Adobe Portable document format (pdf) version is available with the distribution of the programs. Look in the doc/pdf folder for the manual.pdf file. This file can be printed or viewed using Acrobat Reader, available through the Adobe website. The manual has also been translated into html. It is available through the following link. Please note that the translator is not perfect: The pdf form of the manual is much more accurate. Specifically, latex2html failed to translate figure 2.4 and simply printed 2.3 twice.

Man Pages

In the UNIX world, it is comman to have man pages for programs. We have written such a set of man pages, and these are available with the UNIX distribution. The man pages are also a part of the manual.pdf file. Here is a list of the man pages.
  1. Emap
  2. Rmap
  3. Rqtl
  4. Rcross
  5. Qstats
  6. LRmapqtl
  7. SRmapqtl
  8. Zmapqtl
  9. JZmapqtl
  10. MImapqtl
  11. MultiRegress
  12. Prune
  13. Preplot
  14. Eqtl
  15. QTLcart

Perl scripts

QTL Cartographer comes with some perl scripts to automate repetitive tasks and reformat output files. They are available in the doc/scripts subdirectory of the distribution. Here are the man pages that explain what the scripts can do.
  1. Bootstrap.pl is a script for running a bootstrap analysis.
  2. CWTupdate.pl is used with Permute.pl for the comparison-wise thresholds.
  3. EWThreshold.pl is used with Permute.pl for the experiment-wise thresholds.
  4. GetMaxLR.pl is used with Permute.pl for the experiment-wise thresholds.
  5. Model8.pl iterates Zmapqtl to find a stable set of cofactors for composite interval mapping.
  6. Permute.pl is a script for running a permutation test.
  7. Prepraw.pl allows you to reformat and check a Mapmaker data file.
  8. SRcompare.pl will compare the set of cofactors in two SRmapqtl output files.
  9. SSupdate.pl is used with Bootstrap.pl to update the sum and sum of squares for the likelihoods and parameter estimates.
  10. Vert.pl converts text file line endings between Unix, Macintosh and Windows.
  11. Ztrim.pl redisplays Zmapqtl output so that it fits in a terminal window.


We are now posting published data sets to our web site. A list of links to the ftp subdirectories follows. Each directory contains a set of text files of data. Please read the Readme file in the directory for information on the data.
  1. Zeng et al provide data for their paper Genetic architecture of a morphological shape difference between two Drosophila species.
If you have any data that you would like to make available via our server, contact Chris Basten.


From time to time, Chris Basten gives presentations on how to use QTL Cartographer. These presentations are created in Microsoft Powerpoint. The source file for the presentation is available with the distribution of the programs. Look in the doc subdirectory.

Binary Traits

See this for more information on the BTmapqtl module. This is an add-on written in LaurenMcIntyre's lab. BTmapqtl is in the binary directory of the distribution (and is created with a make for the UNIX version).

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