LingPy

lingpy.test.evaluate.EvalMSA

class lingpy.test.evaluate.EvalMSA(gold, test)

Base class for the evaluation of automatic multiple sequence analyses.

Parameters :

gold, test : Multiple

The Multiple objects which shall be compared. The first object should be the gold standard and the second object should be the test set.

Notes

Moste of the scores which can be calculated with help of this class are standard evaluation scores in evolutionary biology. For a close description on how these scores are calculated, see, for example, Thompson1999, List2012, and :evobib:`Rosenberg2009b.

Methods

c_score([mode]) Calculate the column (C) score.
check_swaps() Check for possibly identical swapped sites.
jc_score() Calculate the Jaccard (JC) score.
pir_score() Compute the percentage of identical rows (PIR) score.
sp_score([mode]) Calculate the sum-of-pairs (SP) score.