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hmmemit(1)			 HMMER Manual			    hmmemit(1)

NAME
       hmmemit - sample	sequences from a profile

SYNOPSIS
       hmmemit [options] hmmfile

DESCRIPTION
       The  hmmemit  program samples (emits) sequences from the	profile	HMM(s)
       in hmmfile, and writes them to output.  Sampling	sequences may be  use-
       ful  for	a variety of purposes, including creating synthetic true posi-
       tives for benchmarks or tests.

       The default is to sample	one unaligned sequence from the	core probabil-
       ity  model,  which means	that each sequence consists of one full-length
       domain.	Alternatively, with the	-c option, you can emit	a  simple  ma-
       jority-rule  consensus sequence;	or with	the -a option, you can emit an
       alignment (in which case, you probably also want	to set -N to something
       other than its default of 1 sequence per	model).

       As  another option, with	the -p option you can sample a sequence	from a
       fully configured	HMMER search profile. This means sampling  a  `homolo-
       gous  sequence' by HMMER's definition, including	nonhomologous flanking
       sequences, local	alignments, and	multiple domains per sequence, depend-
       ing on the length model and alignment mode chosen for the profile.

       The  hmmfile may	contain	a library of HMMs, in which case each HMM will
       be used in turn.

       hmmfile may be '-' (dash), which	means reading this  input  from	 stdin
       rather than a file.

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

       -o _f_ Direct the output	sequences to file _f_, rather than to stdout.

       -N _n_ Sample _n_ sequences per model, rather than just one.

OPTIONS	CONTROLLING WHAT TO EMIT
       The default is to sample	N sequences  from  the	core  model.  Alterna-
       tively,	you  may  choose  one (and only	one) of	the following alterna-
       tives.

       -a     Emit an alignment	for each HMM in	the hmmfile rather  than  sam-
	      pling unaligned sequences	one at a time.

       -c     Emit  a plurality-rule consensus sequence, instead of sampling a
	      sequence from the	profile	HMM's  probability  distribution.  The
	      consensus	 sequence is formed by selecting the maximum probabil-
	      ity residue at each match	state.

       -C     Emit a fancier plurality-rule consensus sequence than the	-c op-
	      tion. If the maximum probability residue has p < minl show it as
	      a	lower case 'any' residue (n or x); if p	>=  minl  and  <  minu
	      show  it as a lower case residue;	and if p >= minu show it as an
	      upper case residue.  The default settings	of minu	and  minl  are
	      both  0.0, which means -C	gives the same output as -c unless you
	      also set minu and	minl to	what you want.

       -p     Sample unaligned sequences from the implicit search profile, not
	      from the core model.  The	core model consists only of the	homol-
	      ogous states (between the	begin and end states of	a HMMER	 Plan7
	      model).  The  profile  includes  the  nonhomologous  N, C, and J
	      states, local/glocal and uni/multihit  algorithm	configuration,
	      and the target length model.  Therefore sequences	sampled	from a
	      profile may include nonhomologous	 as  well  as  homologous  se-
	      quences,	and may	contain	more than one homologous sequence seg-
	      ment. By default,	the profile is in multihit local mode, and the
	      target sequence length is	configured for L=400.

OPTIONS	CONTROLLING EMISSION FROM PROFILES
       These options require that you have set the -p option.

       -L _n_ Configure	the profile's target sequence length model to generate
	      a	mean length of approximately <n> rather	than  the  default  of
	      400.

       --local
	      Configure	the profile for	multihit local alignment.

       --unilocal
	      Configure	 the  profile for unihit local alignment (Smith/Water-
	      man).

       --glocal
	      Configure	the profile for	multihit glocal	alignment.

       --uniglocal
	      Configure	the profile for	unihit glocal alignment.

OPTIONS	CONTROLLING FANCY CONSENSUS EMISSION
       These options require that you have set the -C option.

       --minl _x_
	      Sets the minl threshold for showing weakly conserved residues as
	      lower case.  (0 <= x <= 1)

       --minu _x_
	      Sets  the	minu threshold for showing strongly conserved residues
	      as upper case.  (0 <= x <= 1)

OTHER OPTIONS
       --seed _n_
	      Seed the random number generator with _n_, an integer >= 0.   If
	      _n_ is nonzero, any stochastic simulations will be reproducible;
	      the same command will give the same results.  If _n_ is  0,  the
	      random  number  generator	 is seeded arbitrarily,	and stochastic
	      simulations will vary from run to	run of the same	command.   The
	      default  is  0: use an arbitrary seed, so	different hmmemit runs
	      will generate different samples.

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			    hmmemit(1)

NAME | SYNOPSIS | DESCRIPTION | COMMON OPTIONS | OPTIONS CONTROLLING WHAT TO EMIT | OPTIONS CONTROLLING EMISSION FROM PROFILES | OPTIONS CONTROLLING FANCY CONSENSUS EMISSION | OTHER OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

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