evol coevol


Running 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]

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-
  -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 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