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. Seperate 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) 2013 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

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

AUTHOR