hmmstat(1)							   HMMER Manual 							hmmstat(1)

NAME

       hmmstat - display summary statistics for a profile file

SYNOPSIS

       hmmstat [options] <hmmfile>

DESCRIPTION

       The hmmstat utility prints out a tabular file of summary statistics for each profile in <hmmfile>.

       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 HMMER applied an effective sequence number calculation
	      such as the default entropy weighting.

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

       relent 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 HMMER3 models, you expect this value to
	      reflect the default target for entropy-weighting.

       info   Mean information content per match state, in bits.  Probably not useful. Information content is  a  slightly  different  calculation
	      than relative entropy.

       p relE Mean  positional	relative entropy, in bits.  This is a fancier version of the per-match-state relative entropy, taking into account
	      the transition (insertion/deletion) probabilities; it may be a more accurate estimation of the average score contributed	per  model
	      consensus position.

       compKL Kullback-Leibler distance between the model's overall average residue composition and the default background frequency distribution.
	      The higher this number, the more biased the residue composition of the profile is. Highly biased profiles can slow the HMMER3 accel-
	      eration pipeline, by causing too many nonhomologous sequences to pass the filters.

OPTIONS

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

SEE ALSO

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

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

COPYRIGHT

       @HMMER_COPYRIGHT@
       p@HMMER_LICENSE@

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

AUTHOR

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

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 							hmmstat(1)