PRODY

NAME

ProDy - Sequence Evolution and Dynamics Analysis

DESCRIPTION

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

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

Evol: Sequence Evolution and Dynamics Analysis

options:

-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.