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.