Coevolution Application
MSA residue coevolution calculation application.
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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'
|