Running :command:`evol occupancy -h` displays:
usage: evol occupancy [-h] [--quiet] [--examples] [-o STR] [-p STR] [-l STR] [-f STR] [-S] [-X STR] [-Y STR] [-T STR] [-D INT] [-W FLOAT] [-F STR] [-H FLOAT] msa positional arguments: msa 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: -o STR, --occ-axis STR calculate row or column occupancy or both., one of row, col, both (default: row) output options: -p STR, --prefix STR output filename prefix, default is msa filename with _occupancy suffix -l STR, --label STR index for column based on msa label -f STR, --number-format STR number output format (default: %12g) figure options: -S, --save-plot save occupancy plot/s -X STR, --xlabel STR specify xlabel -Y STR, --ylabel STR specify ylabel -T STR, --title STR figure title -D INT, --dpi INT figure resolution (dpi) (default: 300) -W FLOAT, --width FLOAT figure width (inch) (default: 8) -F STR, --figure-format STR figure file format, one of png, pdf, raw, svg, eps, ps, svgz, rgba (default: pdf) -H FLOAT, --height FLOAT figure height (inch) (default: 6)
Running :command:`evol occupancy --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