seq1 seq1.seq
seq2 seq2.seq
mode pp
seq1_pp_op ../my_pp1
seq2_pp_op my_pp2
seq1_sample_ct_op ../my_ct1_sample.txt
seq2_sample_ct_op ../../my_ct2_sample.txt
sample_aln_op ./my_aln_sample.txt
seq1_map_ct_op ../my_map_ct1.txt
seq2_map_ct_op ../../my_map_ct2.txt
map_aln_op ../my_map_aln.txt
nsamp 1000