As a general rule, we suggest creating a separate subdirectory (folder) for each data set and copying the original input files into that subdirectory. This will help to organize your work and preserve your original files. If any exercise goes awry you can delete the subdirectory and start over.
Beginning with the first program you run, a resource file called qtlcart.rc is created and updated for each subsequent program. This file keeps track of all the parameters and file names that you use. In addition, a log file will record which specific parameters were used with which specific programs, and when the programs were run. Thus, the qtlcart.rc file keeps track of the current settings, and the qtlcart.log file records the history of parameter settings. You can look at any of these files or any other files that QTL Cartographer creates by opening them in any text editor.
QTL Cartographer on Macintoshes and Windows-based PCs behaves slightly differently than UNIX host. They maintain one copy of the qtlcart.rc file in the subdirectory (folder) where the applications are located. You can specify a working subdirectory (folder) in any of the QTL Cartographer programs, and this will be recorded in the qtlcart.rc file (see 1.6.1 for details). For the purposes of this tutorial, create a directory called qwork: If you are on a Macintosh or a PC, create it in the directory (folder) one level higher than where the binaries are. If you are on a UNIX machine, create the qwork subdirectory in your root directory.
There is a web page for QTL Cartographer
http://statgen.ncsu.edu/qtlcart/cartographer.htmlwhich is the good place to keep abreast of new information. The README file from the ftp server is linked to the web page. The programs are also linked to the web page, so you can download them using some web browsers. The entire manual as well as the man pages have been been translated into html.