MAPMAKER/EXP is a linkage analysis package designed to help construct primary 
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP 
performs full multipoint linkage analysis (simultaneous estimation of all 
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g.  RFLP-like) markers.  MAPMAKER/EXP is an experimental-cross-only 
successor to the original MAPMAKER program.

MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map 
genes controlling polygenic quantitative traits in F2 intercrosses and BC1 
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL 
can be found in the technical report (included with MAPMAKER/QTL).  

WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/