File: PopStatsCodonSites.bpp

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# ---------------
# Input sequences
# ---------------

# The alphabet to use:
alphabet=Codon(letter=DNA)
genetic_code=Standard

# The sequence file to use (sequences must be aligned!)
input.sequence.file.ingroup=alignment.phy

# The file format:
input.sequence.format.ingroup=Phylip(order=interleaved, type=classic)

# ----------------
# Analysis
# ----------------

pop.stats=CodonSiteStatistics(output.file=alignment.codons.csv),PiN_PiS