evol1
Sequence evolution and dynamics analysis
Overview
usage: evol [-h] [-c] [-v] [-e]
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{search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder} ...
Evol: Sequence Evolution and Dynamics Analysis
options:
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-h, --help -
show this help message and exit
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-c, --cite -
print citation info and exit
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-v, --version -
print ProDy version and exit
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-e, --examples -
show usage examples and exit
subcommands:
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{search,fetch,filter,refine,merge,occupancy,conserv,coevol,rankorder}
- search
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search Pfam with given query
- fetch
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fetch MSA files from Pfam
- filter
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filter an MSA using sequence labels
- refine
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refine an MSA by removing gapped rows/colums
- merge
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merge multiple MSAs based on common labels
- occupancy
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calculate occupancy of rows and columns in MSA
- conserv
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analyze conservation using Shannon entropy
- coevol
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analyze co-evolution using mutual information
- rankorder
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identify highly coevolving pairs of residues
See 'evol <command> -h' for more information on a specific command.