Package Bio :: Package AlignIO :: Module PhylipIO
[hide private]
[frames] | no frames]

Module PhylipIO

source code


AlignIO support for the "phylip" format used in 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).

Note
====
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 3.6 documentation says:

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

At the time of writing, we do nothing special with a dot/period.

Classes [hide private]
  PhylipWriter
Phylip alignment writer.
  PhylipIterator
Reads a Phylip alignment file returning an Alignment object iterator.
Variables [hide private]
  __package__ = 'Bio.AlignIO'