Identify Coevolving Pairs

Refine MSA application.

evol_rankorder(mutinfo, **kwargs)[source]

Identify highly coevolving pairs of residues.

Parameters:mutinfo – mutual information matrix

Input Options

  • zscore (bool) – apply zscore for identifying top ranked coevolving pairs
  • delimiter (str) – delimiter used in mutual information matrix file
  • pdb (str) – PDB file that contains same number of residues as the mutual information matrix, output residue numbers will be based on PDB file
  • msa (str) – MSA file used for building the mutual info matrix, output residue numbers will be based on the most complete sequence in MSA if a PDB file or sequence label is not specified
  • label (str) – label in MSA file for output residue numbers

Output Options

  • numpairs (int) – number of top ranking residue pairs to list, default is 100
  • seqsep (int) – report coevolution for residue pairs that are sequentially separated by input value, default is 3
  • dist (float) – report coevolution for residue pairs whose CA atoms are spatially separated by at least the input value, used when a PDB file is given and –use-dist is true, default is 10.0
  • usedist (bool) – use structural separation to report coevolving pairs
  • outname (str) – output filename, default is mutinfo_rankorder.txt