File: AlnScores.bpp

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DATA=HIV1_REF_2010_gag

input.sequence.file.test   = ../Data/$(DATA)_DNA.fasta
input.sequence.format.test = Fasta
input.sequence.file.ref    = ../Data/$(DATA)_macse_DNA.fasta
input.sequence.format.ref  = Fasta

score.word_size = 3
score.phase     = ATG

output.scores = $(DATA).scores.txt
output.mase = $(DATA).filter.mase
output.sps_thresholds = 0.8