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hmmstat(1)			 HMMER Manual			    hmmstat(1)

NAME
       hmmstat - 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.

       hmmfile may be '-' (a dash character), in which case profiles are  read
       from a stdin pipe instead of from a file.

       The columns are:

       idx    The  index  of  this profile, numbering each profile 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 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 divergence from	the  default  background  fre-
	      quency  distribution to the average composition of the profile's
	      consensus	match states, in bits.	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 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 HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-
       mer.org/).

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	HMMER source distribution, or  see  the	 HMMER
       web page	(http://hmmer.org/).

AUTHOR
       http://eddylab.org

HMMER 3.3			   Nov 2019			    hmmstat(1)

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

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