... Tested and fixed Block.process(*, False, False) In this ivokation process only copies gap patterns, not sequence names. It is equivalent to calling Block._replace_column_contents. Previously this function assumed self is Alignment and that each monomer in self.sequences is visible in columns. This is false for Blocks. author . ... 1 import sys . ... 3 from allpy.alignment import Alignment . 4 from allpy.block import Block . ... 6 p = Alignment ( open ( 'test.fasta' )) . ...