Generates all possible linkage phases between two blocks of markers (or a block and a marker), eliminating equivalent configurations, i.e. configurations with the same likelihood and also considering the two-point information (shared alleles)
generate_all_link_phases_elim_equivalent_haplo(
block1,
block2,
rf.matrix,
ploidy,
max.inc = NULL
)submap with markers of the first block
submap with markers of the second block, or just a single marker identified by its name
matrix obtained with the function rf_list_to_matrix
using the parameter shared.alleles = TRUE
ploidy level (i.e. 4, 6 and so on)
maximum number of allowed inconsistencies (default = NULL: don't check inconsistencies)
Marcelo Mollinari, mmollin@ncsu.edu and Gabriel Gesteira, gdesiqu@ncsu.edu