FLIPS

Evaluates Likelihood of Flipped Marker Orders

Required Input: Chromosome number, ordered list of marker names, number of markers in each tuple to be flipped, LOD threshold.

Description: Given a map of markers in putative order, a LOD threshold, and number of markers per tuple (n), returns the difference in log10likelihood between the original order and each permuted order. Adjacent markers are taken n at a time and rearranged with the log10likelihood recalculated at each step. For n=2, all FLIPS values are displayed. For n>2, only orders whose FLIPS values are less than the specified LOD threshold are shown (i.e. orders with low local support for order).