Check for possibly swapped sites in the alignment.
Parameters : | swap_penalty : int or float
score_mode : { ‘classes’, ‘library’ }
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Returns : | result : bool
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Notes
The method for swap detection is described in detail in [LisB12].
Examples
Load a file containing swaps from the test data.
>>> from lingpy import *
>>> mult = Multiple(get_file('test.msq'))
Align the data, using the progressive approach.
>>> mult.prog_align()
Check for swaps.