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src/c/o/cogent-1.5.3/cogent/core/alignment.py   cogent(Download)
from cogent.format.fasta import fasta_from_alignment
from cogent.format.phylip import phylip_from_alignment
from cogent.format.nexus import nexus_from_alignment
from cogent.parse.gff import GffParser, parse_attributes
from numpy import nonzero, array, logical_or, logical_and, logical_not, \
        Raises exception if invalid alignment
        """
        return nexus_from_alignment(self, seq_type,
                                interleave_len=interleave_len)
 

src/p/y/pycogent-HEAD/cogent/core/alignment.py   pycogent(Download)
from cogent.format.fasta import fasta_from_alignment
from cogent.format.phylip import phylip_from_alignment
from cogent.format.nexus import nexus_from_alignment
from cogent.parse.gff import GffParser, parse_attributes
from numpy import nonzero, array, logical_or, logical_and, logical_not, \
        Raises exception if invalid alignment
        """
        return nexus_from_alignment(self, seq_type,
                                interleave_len=interleave_len)