genome=1org
1orgchr2 adhore_gene_lists/1org/1orgchr2.lst
1orgchr6 adhore_gene_lists/1org/1orgchr6.lst
1orgchr38 adhore_gene_lists/1org/1orgchr38.lst

genome=2org
2orgchr19 adhore_gene_lists/2org/2orgchr19.lst
2orgchr16 adhore_gene_lists/2org/2orgchr16.lst
2orgchr10 adhore_gene_lists/2org/2orgchr10.lst

blast_table=adhore_pairwise.table

output_path=out
cluster_type=collinear

gap_size=20
cluster_gap=20
max_gaps_in_alignment=40
tandem_gap=2

q_value=0.7
prob_cutoff=0.01
anchor_points=3
alignment_method=gg2
multiple_hypothesis_correction=FDR
visualizeGHM=false
visualizeAlignment=true
number_of_threads=1
    