For many of the infer_st_XXX commands it is assumed that only one individual is sampled per species in gene trees. However, the option -a allows multiple alleles to be sampled. For example, if taxa a1 and a2 in gene trees map to taxon a in species tree and taxa b1 and b2 in gene trees map to taxon b in species tree, the following associations should be used in the command parameter:
-a <a:a1,a2; b:b1,b2>