Coevolution Application

MSA residue coevolution calculation application.

prody.apps.evol_apps.evol_coevol.evol_coevol(msa, **kwargs)[source]

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'