# Baba config example

# Valid gap costs:
#   (a) a value: 4 or -1 (will be repeated over the string)
#   (b) a sequence: 1,3,5 or {1, 4, 2} (must have the same length of the string)
#   (c) an empty string: interpreted as sequence starting from 1.

# Valid score tables: PAM250, BLOSUM50, BLOSUM62, VTML160, PENALIZEMISMATCH_1, PENALIZEMISMATCH_2, PENALIZEMISMATCH_3

[simple_dp]
S1=END
s2=SEND
s1_gap_cost=
s2_gap_cost=-4

[needleman_wunsch]
s1=HEAGAWGHEE
s2=PAWHEAE
score_table=BLOSUM62
s1_gap_cost=-6
s2_gap_cost=-6

[smith_waterman]
s1=HEAGAWGHEE
s2=PAWHEAE
score_table=
s1_gap_cost=
s2_gap_cost=

[four_russians]
s1=ATGTCA
s2=ATTAGTCA
[nussinov]
s1=GGGAAAUCC
score_table=