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We describe four improvements we have implemented in a version of the genetic linkage analysis programs in the LINKAGE package: subdivision of recombination classes, better handling of loops, better coordination between the optimization and output routines, and a checkpointing facility. The unifying theme for all the improvements is to store a small amount of data to avoid expensive recomputation of known results. The subdivision of recombination classes improves on a method of Lathrop and Lalouel Am J Hum Genet 1988;42:498-505. The new method of handling loops extends a proposal of Lange and Elston Hum Hered 1975;25:95-105 for loopless pedigrees with multiple nuclear families at the earliest generation. From a practical point of view, the most important improvement may be the checkpointing facility which allows the user to carry out linkage computations that are much longer than the mean-time-to-failure of the underlying computer.
ffer et al. (Sat,) studied this question.