evol conserv


Running evol conserv -h displays:

usage: evol conserv [-h] [--quiet] [--examples] [-n] [-g] [-p STR] [-f STR]
                    [-S] [-H FLOAT] [-W FLOAT] [-F STR] [-D INT]

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-
  -g, --gaps            do not omit gap characters

output options:
  -p STR, --prefix STR  output filename prefix, default is msa filename with
                        _conserv suffix
  -f STR, --number-format STR
                        number output format (default: %12g)

figure options:
  -S, --save-plot       save conservation plot
  -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 raw, png, ps, svgz, eps,
                        pdf, rgba, svg (default: pdf)
  -D INT, --dpi INT     figure resolution (dpi) (default: 300)


Running evol conserv --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