(* Custom Alphabet to Breakinv characters *)
read(custom_alphabet:("ca1.fas", "m1.fas"))
transform((all,custom_to_breakinv:()))
transform((all, dynamic_pam:(locus_breakpoint:20,
locus_indel:(10, 1.5), median:1, swap_med:1)))
build()
swap()
select()
report("breakinv", diagnosis)
report("consensustree", graphconsensus)
exit()
