Provided by: infernal_1.1.2-2_amd64 bug

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) 2016 Howard Hughes Medical Institute.
       Freely distributed under a 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