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.