def process(fs, raw_lines):
headers, sequences = Phylip.decode(raw_lines)
binary_rows = Carbone.get_binary_rows(sequences)
if fs.hud:
return hud.encode(headers, binary_rows) + '\n'
elif fs.phy:
binary_seqs = [''.join(str(x) for x in row) for row in binary_rows]
return Phylip.encode(headers, binary_seqs) + '\n'
