Package Bio :: Package AlignIO :: Module PhylipIO
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Module PhylipIO

source code

AlignIO support for "phylip" format from Joe Felsenstein's PHYLIP tools.

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).

Support for "relaxed phylip" format is also provided. Relaxed phylip differs from standard phylip format in the following ways:

Relaxed phylip is supported by RAxML and PHYML.


In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003) a dot/period (".") in a sequence is interpreted as meaning the same character as in the first sequence. The PHYLIP documentation from 3.3 to 3.69 says:

"a period was also previously allowed but it is no longer allowed, because it sometimes is used in different senses in other programs"

Biopython 1.58 or later treats dots/periods in the sequence as invalid, both for reading and writing. Older versions did nothing special with a dot/period.

Classes [hide private]
Phylip alignment writer.
Reads a Phylip alignment file returning a MultipleSeqAlignment iterator.
Relaxed Phylip format writer.
Relaxed Phylip format Iterator.
Sequential Phylip format Writer.
Sequential Phylip format Iterator.
Variables [hide private]
  _NO_DOTS = 'PHYLIP format no longer allows dots in sequence'
  __package__ = 'Bio.AlignIO'