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| bedplot | Creation of BED and BedGraph custom tracks |
| genomeplot | Creation of Genome Graph files |
| lods1 | LOD score table for chromosome 1 |
| lods2 | LOD score table for chromosome 1 |
| nplplot | Plotting statistics along a chromosome |
| nplplot.multi | Plotting linkage or association statistics for multiple results files |
| nplplot.old | LOD score plotting (old version of nplplot) |
| prepareplot | Prepare input data files for bedplot and genomeplot |