Package Bio :: Package SeqIO :: Module PhylipIO
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Module PhylipIO

source code


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
Write interlaced Phylip sequence alignments
Functions [hide private]
 
PhylipIterator(handle, alphabet=SingleLetterAlphabet())
Reads a Phylip alignment file returning a SeqRecord object iterator
source code
Function Details [hide private]

PhylipIterator(handle, alphabet=SingleLetterAlphabet())

source code 

Reads a Phylip alignment file returning a SeqRecord object iterator

Record identifiers are limited to at most 10 characters.

It only copes with interlaced phylip files! Sequential files won't work where the sequences are split over multiple lines.

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