Table 1 Functions of the AFLPsim package
Function name | Description |
|---|---|
Simulations | |
demosimhybrid | conducts demographic analysis in hybrid populations. |
hybridize | generates multilocus dominant hybrids individuals from parental profiles. |
hybridsim | generates multilocus dominant parental and hybrid individuals. |
Genome scan | |
bayescan | calls Bayescan 2.1 program [12] from R to a set of populations. |
gscan | conducts genome scan on F1 and backcross individuals [10]. |
hybridindex | estimates the hybrid index calling the introgress package. |
Plotting | |
plot.hybridsim | plots phenotypic frequencies of hybrids on a neutral hybridization model. |
plot.demosimhybrid | plots results of ‘demosimhybrid’ function. |
Data manipulation | |
sim2adegenet | converts simulation to the genind format [25]. |
sim2arlequin | writes the input file for Arlequin[26] from the simulation results. |
sim2bayescan | writes the input file for Bayescan[12] from the simulation results. |
sim2popgene | writes the input file for Popgene[27] from the simulation results. |
sim2introgress | converts simulation to the introgress format [16]. |
sim2newhybrids | writes the input file for Newhybrids[8] from the simulation results. |
sim2structure | writes the input file for Structure[28] from the simulation results. |