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| LGS-package | LGS: A package to simulate Linkage Group Selection |
| biasLGS | Bias a vector of allele ratios (LGS) |
| bottleneck | Samples a population to simulate a bottleneck |
| crossLGS | Perform advanced crosses |
| DataStructure | Data structure of LGS output |
| exp2JoinMap | Make input file for JoinMap |
| haplo2string | Convert haplotypes to strings |
| LGS | LGS: A package to simulate Linkage Group Selection |
| normPop | Normalize populations |
| pcMap | A map file for Plasmodium chabaudi |
| plotBins | Plot z-scores of bins of markers |
| plotLGS | Plot the output of a LGS experiment as a genome scan |
| repLGS | Replicate LGS experiments |
| selClones | Reproduce clonally and select a population |
| selDepth | Find depth of a selection valley |
| simLGS | Simulate crosses and apply selection |
| summaryLGS | Summary statistics of an LGS object |
| topClones | Count the most represented clones |
| zbins | z-score: Assessing selection |