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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	start-
	      ing 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  calcula-
	      tion 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 ex-
	      pected (mean) score per consensus	position. This is what the de-
	      fault entropy-weighting method for effective sequence number es-
	      timation 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 ac-
	      count  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 distri-
	      bution.	The  higher  this  number, the more biased the residue
	      composition of the profile is. Highly biased profiles  can  slow
	      the HMMER3 acceleration pipeline,	by causing too many nonhomolo-
	      gous 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  HM-
       MER  distribution  (Userguide.pdf);  or	see  the  HMMER	web page (@HM-
       MER_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)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

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