Pseudomarker Programs

Current Version 2.04 (June 23, 2008)

[ Software manual (Word doc) | Data Format | Tutorial ]


PSEUDOMARKER is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. The main theory underlying these programs is presented in Sen and Churchill (2001).

System requirements

  • Matlab 7.0 (R14) or higher with statistics toolbox (NOTE: Pseudomarker is known to be incompatible with MATLAB version 7.5 (R2007b) on Windows. Pseudomarker should work as expected in earlier and later versions of MATLAB)
  • Windows XP/Linux 9.0/Mac OS-X 10.4 or greater
  • A minimum of 256M of RAM is recommended. You may require more or less depending on the size of your input data and the type of analysis you run.

Warranty Disclaimer and Copyright Notice

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.


The software package is distributed as a zip file. It consists of a number of text files with the extension .m. Engine functions are written in C for better performance. You need to compile these engine functions under Matlab. Follow the steps to install Pseudomarker:

  1. Download the pseudomarker source code zip file
  2. Close Matlab.
  3. Unzip the package into a directory, e.g., c:\pseudomarker
    - To extract in Windows, just double click the file and following the steps. I suggest you to use winzip instead of stuffit to extract.
    - To extract in Mac OS-X 10.4 double click the zip file.
    - In linux, type "unzip pm<version-number>.zip" in the terminal (replacing <version number with the actual version number)
  4. Start Matlab, change directory to c:\pseudomarker (by typing "cd c:\pseudomarker" in Matlab command window).
  5. Set up the C compiler (if you have not done so) by typing "mex -setup". Choose Lcc as the compiler.
  6. Type "make all" in Matlab. This will compile all C modules and put the object code into c:\pseudomarker\private.
  7. Restart Matlab.


The first release of the software (Version 0.9) was written by Saunak Sen. Hao Wu made extensive changes on the code and wrote the software manual. Some C engine functions were borrowed from Karl Broman's R/qtl package.


For problems, questions and suggestions, please contact