(*Chromosome analysis of unannotated sequences*)

read(chromosome:("11mito.fas"))
transform(tcm:(1,2),gap_opening:3)
transform(chromosome:(annotate:(mauve,25.0,0.30,0.01,0.08)))
transform(fixed_states:("mauveout",ignore_polymorphism))
transform(chromosome:(locus_inversion:100,locus_indel:(10,0.9)))
build(100)
swap(threshold:5.0)
select()
set(root:"Taxon11")
report("unann_chrom_diag.txt",diagnosis)
report("unann_chrom_cs.pdf",graphconsensus)
exit()