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# Global variables:
DATA = HIV1_REF_2010_gag
# ---------------
# Input sequences
# ---------------
# The alphabet to use:
# [DNA|RNA|Protein|Generic]
alphabet=Codon(code=Standard, letter=DNA)
# The sequence file to use (sequences must be aligned!)
input.sequence.file=../Data/$(DATA)_DNA.fasta
# The file format:
input.sequence.format=Fasta
# ----------------
# Output sequences
# ----------------
output.sequence.file=$(DATA)_AA.fasta
# The file format:
output.sequence.format=Fasta()
# -----------------------
# Sequences manipulations
# -----------------------
#For example (see manual for a detailed list of available options):
sequence.manip = CoerceToAlignment,RemoveStops,KeepComplete(maxGapAllowed=30%),Translate(code=StandardGeneticCode)
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