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.

SEE ALSO

       See  infernal(1)  for  a  master man page with a list of all the individual man pages for programs in the
       Infernal package.

       For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf);
       or see the Infernal web page ().

COPYRIGHT

       Copyright (C) 2019 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 ().

AUTHOR

       The Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org