A number of software tools for genetic map construction are available (Cheema and Dicks 2009). A broader list of software tools for genetic map development can be found at http://www. nslij-genetics. org/soft/. Here we just choose two software tools for discussion because they are popular amongst our colleagues in the switchgrass community.

MAPMAKER

The MAPMAKER software combines an Expectation-Maximization (EM) algorithm for recombination fraction estimation with a Hidden Markov Model (HMM) method for calculating the expected number of inter-marker recombination events, significantly lowering computation time for large datasets. Marker order estimation is conducted through a pre-processing step that involves a three-point analysis of all linked triples. Once a marker order is found it can be locally optimized through a "ripple" procedure, whereby the order of neighboring markers is reorganized, to check for improvements in the marker order (Lander et al. 1987). MAPMAKER was written for DOS and for UNIX operating systems. It includes an interactive command language that enables data exploration and has been very widely used and cited in the construction of linkage maps for many species including human and major crops. However, since the latest version (V3.0) was released in 1993, the updated version is not available. In switchgrass, an early linkage map was constructed with MAPMAKER (Missaoui et al. 2005b).