# Bio.AlignIO.MsfIO module

Bio.AlignIO support for GCG MSF format.

The file format was produced by the GCG PileUp and and LocalPileUp tools, and later tools such as T-COFFEE and MUSCLE support it as an optional output format.

The original GCG tool would write gaps at ends of each sequence which could be missing data as tildes (`~`), whereas internal gaps were periods (`.`) instead. This parser replaces both with minus signs (`-`) for consistency with the rest of `Bio.AlignIO`.

You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences).

class Bio.AlignIO.MsfIO.MsfIterator(handle, seq_count=None)

  Bases: `AlignmentIterator`

  GCG MSF alignment iterator.

  __next__()

    Parse the next alignment from the handle.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 30
  __static_attributes__ = ('_header',)

Biopython v: 1.86

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