The pedigree and genotypic data must be entered into a single file. A text editor or database system that interfaces with the LINKAGE programs can be used for this. Neither of these programs is supplied with the LINKAGE package.
If you are entering data with a text editor, please consult section 2.8 of this manual for the format to use. The program MAKEPED , not described here, can assist in the construction of the necessary genealogical pointers.
A file describing the loci must be constructed with a text editor or with the program PREPLINK . Please consult section 2.6 for the format of this file.
You must choose the LINKAGE program suitable for the analysis that you wish to undertake. The data and pedigree files constructed in step 1 and step 2 serve as input either directly to the LINKAGE programs or to the LINKAGE CONTROL PROGRAM (LCP), which is a shell for generating command files to control the analysis programs.
The LINKAGE programs contain constants that determine upper limits to the number of loci, alleles, etc. that can be considered simultaneously. Verify that your problem does not exceed the limits established when the program was compiled. If your needs exceed these limits, you can change the constants and recompile the programs. Please consult Chapters 3 and Chapter 4 for a list of the program constants and their meaning.
Because older versions of LINKAGE did not contain provisions for different mutation rates in males and females, you must modify any earlier files by adding a second mutation rate. Also, add the program identifiers required by the LCP shell. See section 2.6 for a description of these modifications.
Data extracted from the CEPH data base with the program SETPED (supplied only in the CEPH program package) can be analyzed with LINKAGE if the file PAR.IN, containing the loci description, as modified as above. Pedigree data is contained in the file PED.IN.