genome=1org
1orgchr1 adhore_gene_lists/1org/1orgchr1.lst
1orgchr2 adhore_gene_lists/1org/1orgchr2.lst
1orgchr3 adhore_gene_lists/1org/1orgchr3.lst
1orgchr4 adhore_gene_lists/1org/1orgchr4.lst
1orgchr5 adhore_gene_lists/1org/1orgchr5.lst
1orgchr6 adhore_gene_lists/1org/1orgchr6.lst
1orgchr7 adhore_gene_lists/1org/1orgchr7.lst
1orgchr8 adhore_gene_lists/1org/1orgchr8.lst
1orgchr9 adhore_gene_lists/1org/1orgchr9.lst
1orgchr10 adhore_gene_lists/1org/1orgchr10.lst
1orgchr11 adhore_gene_lists/1org/1orgchr11.lst
1orgchr12 adhore_gene_lists/1org/1orgchr12.lst
1orgchr13 adhore_gene_lists/1org/1orgchr13.lst
1orgchr14 adhore_gene_lists/1org/1orgchr14.lst
1orgchr15 adhore_gene_lists/1org/1orgchr15.lst
1orgchr16 adhore_gene_lists/1org/1orgchr16.lst

genome=2org
2orgchr3 adhore_gene_lists/2org/2orgchr3.lst
2orgchr1 adhore_gene_lists/2org/2orgchr1.lst
2orgchr5 adhore_gene_lists/2org/2orgchr5.lst
2orgchr18 adhore_gene_lists/2org/2orgchr18.lst
2orgchr2 adhore_gene_lists/2org/2orgchr2.lst
2orgchr17 adhore_gene_lists/2org/2orgchr17.lst
2orgchr22 adhore_gene_lists/2org/2orgchr22.lst
2orgchr7 adhore_gene_lists/2org/2orgchr7.lst
2orgchr15 adhore_gene_lists/2org/2orgchr15.lst
2orgchr8 adhore_gene_lists/2org/2orgchr8.lst
2orgchr13 adhore_gene_lists/2org/2orgchr13.lst
2orgchr9 adhore_gene_lists/2org/2orgchr9.lst
2orgchr11 adhore_gene_lists/2org/2orgchr11.lst
2orgchr12 adhore_gene_lists/2org/2orgchr12.lst
2orgchr20 adhore_gene_lists/2org/2orgchr20.lst
2orgchr4 adhore_gene_lists/2org/2orgchr4.lst
2orgchr23 adhore_gene_lists/2org/2orgchr23.lst
2orgchr19 adhore_gene_lists/2org/2orgchr19.lst
2orgchr24 adhore_gene_lists/2org/2orgchr24.lst
2orgchr16 adhore_gene_lists/2org/2orgchr16.lst
2orgchr27 adhore_gene_lists/2org/2orgchr27.lst
2orgchr10 adhore_gene_lists/2org/2orgchr10.lst
2orgchr26 adhore_gene_lists/2org/2orgchr26.lst
2orgchr6 adhore_gene_lists/2org/2orgchr6.lst
2orgchr21 adhore_gene_lists/2org/2orgchr21.lst
2orgchr30 adhore_gene_lists/2org/2orgchr30.lst
2orgchr14 adhore_gene_lists/2org/2orgchr14.lst
2orgchr25 adhore_gene_lists/2org/2orgchr25.lst
2orgchr28 adhore_gene_lists/2org/2orgchr28.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
    