Bio.Align.phylip module

Bio.Align support for the alignment format for input files for PHYLIP tools.

You are expected to use this module via the Bio.Align functions.

class Bio.Align.phylip.AlignmentWriter(target, mode='w')

Bases: Bio.Align.interfaces.AlignmentWriter

Clustalw alignment writer.

format_alignment(alignment)

Return a string with a single alignment in the Phylip format.

class Bio.Align.phylip.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Reads a Phylip alignment file and returns an Alignment iterator.

Record names are limited to at most 10 characters.

The parser determines from the file contents if the file format is sequential or interleaved, and parses the file accordingly.

For more information on the file format, please see: http://evolution.genetics.washington.edu/phylip/doc/sequence.html http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles

__init__(source)

Create an AlignmentIterator object.

Arguments:

• source - input data or file name

__abstractmethods__ = frozenset({})