This documentation is for version 2.0.dev, which is not released yet.
Basic class for dealing with the pairwise alignment of sequences.
Parameters : | infile : file
merge_vowels : bool (default=True)
comment : char (default=’#’)
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Notes
In order to read in data from text files, two different file formats can be used along with this class: the PSQ-format, and the PSA-format.
This class inherits the methods of the Pairwise class.
Attributes
taxa | list | A list of tuples containing the taxa of all sequence pairs. |
seqs | list | A list of tuples containing all sequence pairs. |
tokens | list | A list of tuples containing all sequence pairs in a tokenized form. |
Methods
align([gop, scale, mode, factor, ...]) | Align a pair of sequences or multiple sequence pairs. |
output([fileformat, filename]) | Write the results of the analyses to a text file. |