linkage user's guide (version 5.2)

3.5 CILINK

Purpose

The program CILINK performs the same function as ILINK but is restricted to three-generation pedigrees and codominant marker loci. Only recombination rates, and the female/male genetic distance, can be iterated.

Using the Program

CILINK functions with the program CFACTOR. The calling order is: 

     CFACTOR
     CILINK
The input files for this suite of programs are: 
     PEDFILE
     DATAFILE
The output files are: 
     FINAL
     OUTFILE
     STREAM
TEMPPED and TEMPDAT are temporary files produced by CFACTOR for input to CILINK.

Program Constants Specific to CILINK

CILINK contains many of the program constants that ILINK does for controlling numerical maximization.

Datafile Structure

The program code for CILINK is 1. Otherwise, the DATAFILE format is the same as that for the ILINK program except that all loci must be codominant. Either allele numbers or binary codes can be used to describe the loci. Only recombination rates, and the female/male genetic distance ratio can be estimated.

Comments: Recoding reduces the number of alleles at each locus; hence CILINK uses arbitrary gene frequencies. This can affect the likelihood values slightly when some parent or grandparent genotypes are missing.

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