Running :command:`evol filter -h` displays:
usage: evol filter [-h] [--quiet] [--examples] (-s | -e | -c) [-F] [-o STR] [-f STR] [-z] msa word [word ...] positional arguments: msa MSA filename to be filtered word word to be compared to sequence label optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit filtering method (required): -s, --startswith sequence label starts with given words -e, --endswith sequence label ends with given words -c, --contains sequence label contains with given words filter option: -F, --full-label compare full label with word(s) output options: -o STR, --outname STR output filename, default is msa filename with _refined suffix -f STR, --format STR output MSA file format, default is same as input -z, --compressed gzip refined MSA output
Running :command:`evol filter --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