MapMaker 3 – Genetic Linkage Analysis & Mapping Genes Complex Traits

MapMaker 3


MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

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).


The Broad Institute, Cambridge, MA




  • Linux / Mac OsX / Windows





Please use Lander et al. 1987 for MAPMAKER/EXP, and Paterson et al. 1988 for
MAPMAKER/QTL. Please also cite:

S. Lincoln, M. Daly, and E. Lander: Constructing Genetic Maps with MAPMAKER/EXP
3.0. (1992) Whitehead Institute Technical Report. 3rd edition.

S. Lincoln, M. Daly, and E. Lander: Mapping Genes Controlling Quantitative
Traits with MAPMAKER/QTL 1.1. (1992) Whitehead Institute Technical Report. 2nd