Running :command:`evol refine -h` displays:
usage: evol refine [-h] [--quiet] [--examples] [-l STR] [-s FLOAT] [-c FLOAT] [-r FLOAT] [-k] [-o STR] [-f STR] [-z] msa positional arguments: msa MSA filename to be refined optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit refinement options: -l STR, --label STR sequence label, UniProt ID code, or PDB and chain identifier -s FLOAT, --seqid FLOAT identity threshold for selecting unique sequences -c FLOAT, --colocc FLOAT column (residue position) occupancy -r FLOAT, --rowocc FLOAT row (sequence) occupancy -k, --keep keep columns corresponding to residues not resolved in PDB structure, applies label argument is a PDB identifier 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 refine --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