Running :command:`evol rankorder -h` displays:
usage: evol rankorder [-h] [--quiet] [--examples] [-z] [-d STR] [-p STR] [-m STR] [-l STR] [-n INT] [-q INT] [-t FLOAT] [-u] [-o STR] mutinfo positional arguments: mutinfo mutual information matrix optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit input options: -z, --zscore apply zscore for identifying top ranked coevolving pairs -d STR, --delimiter STR delimiter used in mutual information matrix file -p STR, --pdb STR PDB file that contains same number of residues as the mutual information matrix, output residue numbers will be based on PDB file -m STR, --msa STR MSA file used for building the mutual info matrix, output residue numbers will be based on the most complete sequence in MSA if a PDB file or sequence label is not specified -l STR, --label STR label in MSA file for output residue numbers output options: -n INT, --num-pairs INT number of top ranking residue pairs to list (default: 100) -q INT, --seq-sep INT report coevolution for residue pairs that are sequentially separated by input value (default: 3) -t FLOAT, --min-dist FLOAT report coevolution for residue pairs whose CA atoms are spatially separated by at least the input value, used when a PDB file is given and --use-dist is true (default: 10.0) -u, --use-dist use structural separation to report coevolving pairs -o STR, --outname STR output filename, default is mutinfo_rankorder.txt
Running :command:`evol rankorder --examples` displays:
Sequence coevolution analysis involves several steps that including retrieving data and refining it for calculations. These steps are illustrated below for RnaseA protein family. Search Pfam database: $ evol search 2w5i Download Pfam MSA file: $ evol fetch RnaseA Refine MSA file: $ evol refine RnaseA_full.slx -l RNAS1_BOVIN --seqid 0.98 --rowocc 0.8 Checking occupancy: $ evol occupancy RnaseA_full.slx -l RNAS1_BOVIN -o col -S Conservation analysis: $ evol conserv RnaseA_full_refined.slx Coevolution analysis: $ evol coevol RnaseA_full_refined.slx -S -c apc Rank order analysis: $ evol rankorder RnaseA_full_refined_mutinfo_corr_apc.txt -p 2w5i_1-121.pdb --seq-sep 3