Help; print a brief reminder of command line usage and all available
Emit a consensus sequence, instead of sampling a sequence from the
profile HMMs probability distribution. The consensus sequence is
formed by selecting the maximum probability residue at each match
Direct the output sequences to file
<f>, rather than to
Sample sequences from the implicit profile, not from the core model.
The core model consists only of the homologous 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 sequences, and may contain more than one homologous
sequence segment. By default, the profile is in multihit local mode,
and the target sequence length is configured for L=400. To change
these defaults, see Options Controlling Emission from Profiles, below.
<n> sequences, rather than just one.
All these options require that the -p option is also set.
-L <n> Configure the profiles 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/Waterman).
--glocal Configure the profile for multihit glocal alignment.
--uniglocal Configure the profile for unihit glocal alignment.
--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 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@).
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 http://eddylab.org
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