Bio.AlignIO.PhylipIO module

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:

• 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.

class Bio.AlignIO.PhylipIO.PhylipWriter(handle)

Bases: SequentialAlignmentWriter

Phylip alignment writer.

write_alignment(alignment, id_width=_PHYLIP_ID_WIDTH)

Use this to write (another) single alignment to an open file.

This code will write interlaced alignments (when the sequences are longer than 50 characters).

Note that record identifiers are strictly truncated to id_width, defaulting to the value required to comply with the PHYLIP standard.

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

class Bio.AlignIO.PhylipIO.PhylipIterator(handle, seq_count=None)

Bases: AlignmentIterator

Reads a Phylip alignment file returning a MultipleSeqAlignment 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

id_width = 10

__next__()

Parse the next alignment from the handle.

class Bio.AlignIO.PhylipIO.RelaxedPhylipWriter(handle)

Bases: PhylipWriter

Relaxed Phylip format writer.

write_alignment(alignment)

Write a relaxed phylip alignment.

class Bio.AlignIO.PhylipIO.RelaxedPhylipIterator(handle, seq_count=None)

Bases: PhylipIterator

Relaxed Phylip format Iterator.

class Bio.AlignIO.PhylipIO.SequentialPhylipWriter(handle)

Bases: SequentialAlignmentWriter

Sequential Phylip format Writer.

write_alignment(alignment, id_width=_PHYLIP_ID_WIDTH)

Write a Phylip alignment to the handle.

class Bio.AlignIO.PhylipIO.SequentialPhylipIterator(handle, seq_count=None)

Bases: PhylipIterator

Sequential Phylip format Iterator.

The sequential format carries the same restrictions as the normal interleaved one, with the difference being that the sequences are listed sequentially, each sequence written in its entirety before the start of the next. According to the PHYLIP documentation for input file formatting, newlines and spaces may optionally be entered at any point in the sequences.

__next__()

Parse the next alignment from the handle.

Bio.AlignIO.PhylipIO.sanitize_name(name, width=None)

Sanitise sequence identifier for output.

Removes the banned characters “[]()” and replaces the characters “:;” with “|”. The name is truncated to “width” characters if specified.