Ubuntu Manpage: cmstat - summary statistics for a covariance model file

NAME

       cmstat - summary statistics for a covariance model file

SYNOPSIS

       cmstat [options] <cmfile>

DESCRIPTION

The cmstat utility prints out a tabular file of summary statistics for each covariance model in <cmfile>.

<cmfile> may be '-' (a dash character), in which case CMs are read from a <stdin> pipe instead of from a
file.

By default, cmstat prints general statistics of the model and the alignment it was built from, one line
per model in a tabular format. The columns are:

idx The index of this profile, numbering each on in the file starting from 1.

name The name of the profile.

accession
The optional accession of the profile, or "-" if there is none.

nseq The number of sequences that the profile was estimated from.

eff_nseq
The effective number of sequences that the profile was estimated from, after Infernal applied an
effective sequence number calculation such as the default entropy weighting.

clen The length of the model in consensus residues (match states).

W The expected maximum length of a hit to the model.

bps The number of basepairs in the model.

bifs The number of bifurcations in the model.

model What type of model will be used by default in cmsearch and cmscan for this profile, either "cm" or
"hmm". For profiles with 0 basepairs, this will be "hmm" (unless the --nohmmonly option is used).
For all other profiles, this will be "cm".

rel entropy, cm:
Mean relative entropy per match state, in bits. This is the expected (mean) score per consensus
position. This is what the default entropy-weighting method for effective sequence number
estimation focuses on, so for default Infernal, this value will often reflect the default target
for entropy-weighting. If the "model" field for this profile is "hmm", this field will be "-".

rel entropy, hmm:
Mean relative entropy per match state, in bits, if the CM were transformed into an HMM
(information from structure is ignored). The larger the difference between the CM and HMM
relative entropy, the more the model will rely on structural conservation relative sequence
conservation when identifying homologs.

If the model(s) in <cmfile> have been calibrated with cmcalibrate the -E, -T, and -Z <n> options can be
used to invoke an alternative output mode, reporting E-values and corresponding bit scores for a
specified database size of <n> megabases (Mb). If the model(s) have been calibrated and include Rfam GA,
TC, and/or NC bit score thresholds the --cut_ga, --cut_tc, and/or --cut_nc options can be used to display
E-values that correspond to the bit score thresholds. Separate bit scores or E-values will be displayed
for each of the four possible CM search algorithm and model configuration pairs: local Inside, local CYK,
glocal Inside and glocal CYK.

For profiles with zero basepairs (those with "hmm" in the "model" field), any E-value and bit score
statistics will pertain to the profile HMM filter, instead of to the CM. This is also true for all
profiles if the --hmmonly option is used.

OPTIONS

       -h     Help; print a brief reminder of command line usage and all available options.

       -E <x1>
              Report bit scores that correspond to an E-value of <x1> in a database of <x> megabases (Mb), where
              <x> is 10 by default but settable with the -Z <x> option.

       -T <x1>
              Report  E-values that correspond to a bit score of <x1> in a database of <x> megabases (Mb), where
              <x> is 10 by default but settable with the -Z <x> option.

       -Z <x> With the -E, -T, --cut_ga, --cut_nc, and --cut_tc options, calculate E-values  as  if  the  target
              database size was <x> megabases (Mb). By default, <x> is 10.

       --cut_ga
              Report  E-values  that  correspond to the GA (Rfam gathering threshold) bit score in a database of
              <x> megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.

       --cut_tc
              Report E-values that correspond to the TC (Rfam trusted cutoff) bit score in  a  database  of  <x>
              megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.

       --cut_nc
              Report  E-values  that  correspond  to  the  NC (Rfam noise cutoff) bit score in a database of <x>
              megabases (Mb), where <x> is 10 by default but settable with the -Z <x> option.

       --key <s>
              Only print statistics for CM with name or accession <s>, skip all other models in <cmfile>.

       --hmmonly
              Print statistics on the profile HMM filters for all profiles, instead of  the  CMs.  This  can  be
              useful if you plan to use the --hmmonly option to cmsearch or cmscan.

       --nohmmonly
              Always print statistics on the CM for each profile, even for those with zero basepairs.

COPYRIGHT

       Copyright (C) 2023 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       For additional information on copyright and licensing, see the file called  COPYRIGHT  in  your  Infernal
       source distribution, or see the Infernal web page (http://eddylab.org/infernal/).

AUTHOR