Abstract
There is now a wide choice of software available for linkage analysis. The most well known packages are briefly reviewed here. The package with the most extensive range of analyses is GENEHUNTER, but for many of its functions there are other programs with better performance. These include FASTLINK and VITESSE for parametric analysis ALLEGRO and MERLIN for non-parametric analysis and SOLAR for variance components analysis. The computational limits of current approaches can be improved with SIMWALK2 and the promising new SUPERLINK program. Directions for future work include improved user interfaces and consensus formats for data input and exchange.
Highlights
There is a wide choice of methods and software available for mapping genes by linkage
Whether one applies single- or multi-point analysis of a disease or quantitative trait, VITESSE is a faster package;[4,5] FASTLINK continues to be more efficient for pedigrees containing inbreeding loops
Linkage analysis is applied to a large number of small pedigrees with unknown mode of inheritance
Summary
There is a wide choice of methods and software available for mapping genes by linkage. Linkage analysis is applied to a small number of large pedigrees in which the trait exhibits a strongly Mendelian mode of inheritance. The most flexible package for these analytical methods remains FASTLINK,[1,2] which is functionally equivalent to the original LINKAGE package.[3] For most pedigree structures, whether one applies single- or multi-point analysis of a disease or quantitative trait, VITESSE is a faster package;[4,5] FASTLINK continues to be more efficient for pedigrees containing inbreeding loops.
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