Running :command:`evol coevol -h` displays:
usage: evol coevol [-h] [--quiet] [--examples] [-n] [-c STR] [-m STR] [-t] [-p STR] [-f STR] [-S] [-L FLOAT] [-U FLOAT] [-X STR] [-T STR] [-D INT] [-H FLOAT] [-W FLOAT] [-F STR] msa positional arguments: msa refined MSA file optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit calculation options: -n, --no-ambiguity treat amino acids characters B, Z, J, and X as non- ambiguous -c STR, --correction STR also save corrected mutual information matrix data and plot, one of apc, asc -m STR, --normalization STR also save normalized mutual information matrix data and plot, one of sument, minent, maxent, mincon, maxcon, joint output options: -t, --heatmap save heatmap files for all mutual information matrices -p STR, --prefix STR output filename prefix, default is msa filename with _coevol suffix -f STR, --number-format STR number output format (default: %12g) figure options: -S, --save-plot save coevolution plot -L FLOAT, --cmin FLOAT apply lower limits for figure plot -U FLOAT, --cmax FLOAT apply upper limits for figure plot -X STR, --xlabel STR specify xlabel, by default will be applied on ylabel -T STR, --title STR figure title -D INT, --dpi INT figure resolution (dpi) (default: 300) -H FLOAT, --height FLOAT figure height (inch) (default: 6) -W FLOAT, --width FLOAT figure width (inch) (default: 8) -F STR, --figure-format STR figure file format, one of svgz, rgba, png, pdf, eps, svg, ps, raw (default: pdf)
Running :command:`evol coevol --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