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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignIO-module.html">Package AlignIO</a> ::
Module PhylipIO
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<h1 class="epydoc">Module PhylipIO</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.AlignIO.PhylipIO-pysrc.html">source code</a></span></p>
<pre class="literalblock">
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).
Support for "relaxed phylip" format is also provided. Relaxed phylip differs
from standard phylip format in the following ways:
* No whitespace is allowed in the sequence ID.
* No truncation is performed. Instead, sequence IDs are padded to the longest
ID length, rather than 10 characters. A space separates the sequence
identifier from the sequence.
Relaxed phylip is supported by RAxML and PHYML.
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 documentation from 3.3 to 3.69
http://evolution.genetics.washington.edu/phylip/doc/sequence.html 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.
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<a href="Bio.AlignIO.PhylipIO.PhylipWriter-class.html" class="summary-name">PhylipWriter</a><br />
Phylip alignment writer.
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<a href="Bio.AlignIO.PhylipIO.PhylipIterator-class.html" class="summary-name">PhylipIterator</a><br />
Reads a Phylip alignment file returning a MultipleSeqAlignment
iterator.
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<a href="Bio.AlignIO.PhylipIO.RelaxedPhylipWriter-class.html" class="summary-name">RelaxedPhylipWriter</a><br />
Relaxed Phylip format writer
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<a href="Bio.AlignIO.PhylipIO.RelaxedPhylipIterator-class.html" class="summary-name">RelaxedPhylipIterator</a><br />
Relaxed Phylip format Iterator
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<a name="_PHYLIP_ID_WIDTH"></a><span class="summary-name">_PHYLIP_ID_WIDTH</span> = <code title="10">10</code>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.AlignIO'"><code class="variable-quote">'</code><code class="variable-string">Bio.AlignIO</code><code class="variable-quote">'</code></code>
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