# base inference on alignments in the middle 50 percentile
# by percent-identity
min_identity       = 25.0%    # 25th percentile
max_identity       = 75.0%    # 75th percentile

# scale scores so max substitution will be 100 and only use
# alignments scoring as well as 20 substitutions
inference_scale    = 100      # score for max substitution
hsp_threshold      = 20*inference_scale
gapped_threshold   = hsp_threshold

# allow substitution score inference to iterate at most
# 20 times;  don't perform gap score inference
max_sub_iterations = 20
max_gap_iterations = 0
gap_open_penalty   = 4*inference_scale
gap_extend_penalty = 0.3*inference_scale