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