Computer programs for use in linkage analysis

During the last couple of years, I have written several computer programs to aid in the analysis of various types of linkage data. All of the programs use maximum likelihood equations to determine recombinational distances. I am in the slow process of consolidating several together into a few generalized programs and plan to port these to at least IBM compatible systems. Rather than an in-depth discussion of each, a brief description for the currently available programs follows. Please contact me if you are interested in obtaining copies of any or all of these.

Linkage-a program that analyzes multi-point (up to 10) backcross data. Output includes total and percent of each gene class; genotype, number, total, and expected total for each crossover class; and paired recombinational values.

ml-a computerized version of Allard's maximum likelihood equations. Most of the equations have been entered, although any additional equations can be added rather simply. Once the desired equation is selected and the number in each phenotypic or genotypic class is entered, the recombinational value and its standard error are calculated and displayed.

ml-rfp-a program to analyze restriction fragment length polymorphism data. The current version accepts segregation data for dominant, recessive, and co-dominant traits, in backcross and F2 populations. Any combination of traits and populations can be analyzed. Also, any locus or subset of loci can be analyzed. Output includes the segregation of each locus within the population, as well as its segregation and recombination value with all other loci being analyzed.

Dave Hoisington

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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