Improvements to the Flipper Genetic Mapper

The original Flipper mapping program was able to order tens of thousands of genetic markers in linear running time, but it was very sensitive to genotyping errors and missing data.  Therefore, it was not reliable with real genotyping data.  Several changes have overcome this sensitivity, permitting more robust mapping with realistic data while retaining the linear-time ordering for most markers.  The changes include a smaller banding increment between iterations, annealed joins of free ends, restricting insertions to require a free end, testing proposed joins with parallel arrays before committing them to the map arrays, identification and correction of frozen-out linkage groups, and identification and correction of misplaced markers at gap boundaries.  The last two changes address the situation where an erroneously genotyped marker cannot be attached to the proper end of a growing linkage group because there are always closer correctly genotyped markers.  Results of simulations detail Flipper’s response to genotyping errors and gaps within linkage groups.