Software

Pseudomarker programs

Current Version 2.04 (June 23, 2008)

Introduction

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.

Installation

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

Download

Click here to download the program for free. You will be asked to fill out a simple registration form. I'm sorry that you have to fill out this form every time you download the software.

Manual

Here is the software manual as a Microsoft Word document.  

Authors

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.

Contact

For problems, questions and suggestions, please contact pseudomarker@jax.org.