Evol Applications

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

• evol coevol
• evol conserv
• evol fetch
• evol filter
• evol merge
• evol occupancy
• evol rankorder
• evol refine
• evol search

Running evol command will provide a description of applications:

$ evol

usage: evol [-h] [-c] [-v] [-e]
            
            {search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder}
            ...

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

subcommands:
  {search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder}
    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