Flipper—a General Genetic Mapping Package

Flipper is a set of programs for mapping genetic markers and for simulating mapping experiments.  This first release is intended for three kinds of mapping experiments: deletion, backcross, and recombinant inbred.  The latter can be any generation from F2 onward.  The mapper can process any experiment that can be phrased in terms of deletion from a parental monoploid genotype with one allele per locus.  This condition is not as restrictive as it looks: A backcross is expressed as deletion from the nonrecurrent parent’s haploid genotype, using the haploid chromosome number, while a recombinant inbred is expressed as deletion from a “monoploid” having twice the actual haploid chromosome number and where each parent’s allele is treated as an independent locus.  Thus the mapper does not care if the inbred parents of a recombinant inbred population differ in gene order, so long as recombination is not too impeded by structural heterozygosity; it reconstructs and outputs all parental linkage groups.  The next version of the mapper will also accommodate polyploid deletion populations with combinations of simplex and multiplex markers.

The mapper implements a variant of Kruskal’s minimum spanning tree algorithm and runs in polynomial (superquadratic on average) time.  It has successfully recovered the true map order for up to 26000 loci in simulations, without the production of intermediary framework maps.  Its internal data structures preclude the formation of branched linkage groups.  It does not require the prior assignment of markers to linkage groups, but it does require the base chromosome number.  Although this version is single-threaded, multiple instances of it can be run in parallel on sister mapping populations in a multiprocessor environment and later combined, to speed up the mapping of very large populations.

The simulators can construct mapping populations for deletion, backcross, and recombinant inbred experiments, with or without segregation distortion, missing data, and typing errors.  The deletion simulator can handle a chromosome-structurally heterozygous polyploid parent..