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hmmstat(1)			 HMMER Manual			    hmmstat(1)

       hmmstat - display summary statistics for	a profile file

       hmmstat [options] _hmmfile_

       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.

	      The optional accession of	the profile, or	"-" if there is	none.

       nseq   The number of sequences that the profile was estimated from.

	      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.

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

       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-


       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@).

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147	USA

HMMER @HMMER_VERSION@		 @HMMER_DATE@			    hmmstat(1)


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