$ python Python_CAP3_contig_poly_DIS_Feb_27_2004.py
Enter the mismatch file name : L_ABC_Contigs_All.aln.MM
Enter the contig info file name : tomato_ABC.cap3.out.Info
Distinguish by (p)refix or (s)uffix? : p
Please input the size of the prefix : 1
Specify Group 1
Group 1 has []
Please input element : B
Do you want to add more? (y/n) : n
Specify Group 2
Group 2 has []
Please input element : A
Do you want to add more? (y/n) : y
Group 2 has ['A']
Please input element : C
Do you want to add more? (y/n) : n

........ [ after you enter last "n" program will start SNP/INDEL search ]

$ cp deletions.good B_vs_AC_deletions.good
$ cp insertions.good B_vs_AC_insertions.good
$ cp substitutions.good B_vs_AC_substitutions.good

Genotype "C" versus "A" and "B"