Conservation Application

Calculate conservation in an MSA using Shannon entropy.

evol_conserv(msa, **kwargs)[source]

Analyze conservation using Shannon entropy.

Parameters:msa – refined MSA file

Calculation Options

  • ambiguity (bool) – treat amino acids characters B, Z, J, and X as non- ambiguous, default is True
  • omitgaps (bool) – do not omit gap characters, default is True

Output Options

  • prefix (str) – output filename prefix, default is msa filename with _conserv suffix
  • numformat (str) – number output format, default is '%12g'