Evol Applications

Evol applications are command line programs that automate retrieval, refinement, and analysis of multiple sequence alignments:

Running evol command will provide a description of applications:

$ evol
usage: evol [-h] [-c] [-v] [-e]

Evol: Sequence Evolution and Dynamics Analysis

optional arguments:
  -h, --help            show this help message and exit
  -c, --cite            print citation info and exit
  -v, --version         print ProDy version and exit
  -e, --examples        show usage examples and exit

    search              search Pfam with given query
    fetch               fetch MSA files from Pfam
    filter              filter an MSA using sequence labels
    refine              refine an MSA by removing gapped rows/colums
    merge               merge multiple MSAs based on common labels
    occupancy           calculate occupancy of rows and columns in MSA
    conserv             analyze conservation using Shannon entropy
    coevol              analyze co-evolution using mutual information
    rankorder           identify highly coevolving pairs of residues

See 'evol <command> -h' for more information on a specific command.

Detailed information on a specific application can be obtained by typing the command and application names as evol search -h.

Running prody search application as follows will search Pfam database for protein families that match the proteins in PDB structure 2w5i:

$ evol search 2w5i