3 GET STARTED

3.1 Installation

Following the following steps for installation.

è Make a new fold in your computer, and give the fold name, such as INTERQTL;

è Unzip the file interqtl.zip into the folder.

Make sure the following files are present in the folder. INTERQTL will not work properly if one or more of these files are missing.

1) simuQTL.exe This is an executable file that simulates markers and trait values for mapping populations

2) bayesQTL.exe This is an executable file that conducts Bayesian analysis

3) interqtl.exe This is an executable file that provides a single-document editor for input files and runs simulation and Bayesian analysis modules in Windows

3) pedigree.txt This is a text file that contains pedigree information. You must get the pedigree file ready before you start the analysis.

The following files should also be ready and in correct formats with real-data QTL mapping whereas they are automatically generated in simulation approaches. Users may find examples of these files in the folder that provide convenience for beginners to use INTERQTL. Simply follow the formats of these example files to prepare yours.

4) genome.txt This is a text file that contains genome information generated using default parameters

5) f1.txt This is a text file that contains F1 marker genotypes generated using default parameters

6) markers.txt This is a text file that contains progeny marker genotypes generated using default parameters

7) pheno.txt This is a text file that contains trait values of all progeny generated using default parameters

3.2 Run INTERQTL in Windows

Follow these steps to run INTERQTL in WINDOWS

è Go to the fold that you have unzipped interqtl.zip.

è Make sure that required files are ready and in correct formats

è Locate the executable file InterQTL.exe and double click it.

You may or may not need the following DLL files. If you have difficulty running the program, make sure that these files are present in the directory where you run the program. If not, please contact us for them.

1) cc3250.dll

2) MFC42D.DLL

3) MFCO42D.DLL

4) MSVCRTD.DLL

5) MSVCIRTD.DLL

3.3 Run INTERQTL in DOS

As we have mentioned before, SimuQTL.exe and bayesQTL.exe can be run separately in DOS. Before you run SimuQTL.exe for simulation, you must prepare a “simu_Al.txt” file manually. Before you run bayesQTL.exe for Bayesian analysis, you’ll have to prepare a “mult_Al.txt” manually. Refer the Section 5 for how to prepare these two files.