1 #pgm mol matrix g_open g_ext fr_shft e_cut ktup
2 # -n/-p -s -e -f -h/-j -E argv[3]
3 fasta prot bl50 -10 -2 - 10.0 2
4 fasta dna +5/-4 -14 -4 - 2.0 6
5 ssearch prot bl50 -10 -2 - 10.0 -
6 ssearch dna +5/-4 -14 -4 - 2.0 -
7 fastx prot BL50 -12 -2 -20 5.0 2
8 fasty prot BL50 -12 -2 -20/-24 5.0 2
9 tfastx dna BL50 -14 -2 -20 5.0 2
10 tfasty dna BL50 -14 -2 -20/-24 5.0 2
11 fasts prot MD20-MS - - - 5.0 -
12 tfasts prot MD10-MS - - - 2.0 -
13 fastf prot MD20 - - - 5.0 -
14 tfastf prot MD10 - - - 2.0 -
15 fastm prot MD20 - - - 5.0 -
16 tfastm prot MD10 - - - 2.0 -