Coevolution Application

MSA residue coevolution calculation application.

evol_coevol(msa, **kwargs)

Analyze co-evolution using mutual information.

Parameters:msa – refined MSA file

Calculation Options

Parameters:

• ambiguity (bool) – treat amino acids characters B, Z, J, and X as non- ambiguous, default is True
• correction (str) – also save corrected mutual information matrix data and plot, one of 'apc', 'asc'
• normalization (str) – also save normalized mutual information matrix data and plot, one of 'sument', 'minent', 'maxent', 'mincon', 'maxcon', 'joint'

Output Options

Parameters:

• heatmap (bool) – save heatmap files for all mutual information matrices
• prefix (str) – output filename prefix, default is msa filename with _coevol suffix
• numformat (str) – number output format, default is '%12g'