xenial (1) hmmbuild.1.gz

Provided by: hmmer_3.1b2-2_amd64 bug

NAME

       hmmbuild - construct profile HMM(s) from multiple sequence alignment(s)

SYNOPSIS

       hmmbuild [options] <hmmfile_out> <msafile>

DESCRIPTION

       For  each  multiple  sequence  alignment  in  <msafile>  build  a  profile  HMM and save it to a new file
       <hmmfile_out>.

       <msafile> may be '-' (dash), which means reading this input from stdin rather than a file.  To  use  '-',
       you  must also specify the alignment file format with --informat <s>, as in --informat stockholm (because
       of a current limitation in our implementation, MSA file formats cannot be autodetected in a nonrewindable
       input stream.)

       <hmmfile_out>  may  not  be  '-' (stdout), because sending the HMM file to stdout would conflict with the
       other text output of the program.

OPTIONS

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

       -n <s> Name the new profile <s>.  The default is to use the name of the alignment (if one is  present  in
              the  msafile,  or,  failing  that,  the  name  of  the hmmfile.  If msafile contains more than one
              alignment, -n doesn't work, and every alignment must have a name annotated in the msafile  (as  in
              Stockholm #=GF ID annotation).

       -o <f> Direct the summary output to file <f>, rather than to stdout.

       -O <f> After  each  model is constructed, resave annotated, possibly modified source alignments to a file
              <f> in Stockholm format.  The alignments are annotated with a reference annotation line indicating
              which  columns were assigned as consensus, and sequences are annotated with what relative sequence
              weights were assigned. Some residues of  the  alignment  may  have  been  shifted  to  accommodate
              restrictions  of  the  Plan7  profile architecture, which disallows transitions between insert and
              delete states.

OPTIONS FOR SPECIFYING THE ALPHABET

       The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at the composition  of  the
       msafile.   Autodetection  is normally quite reliable, but occasionally alphabet type may be ambiguous and
       autodetection can fail (for instance, on tiny toy alignments of just a few residues). To avoid  this,  or
       to increase robustness in automated analysis pipelines, you may specify the alphabet type of msafile with
       these options.

       --amino
              Specify that all sequences in msafile are proteins.

       --dna  Specify that all sequences in msafile are DNAs.

       --rna  Specify that all sequences in msafile are RNAs.

OPTIONS CONTROLLING PROFILE CONSTRUCTION

       These options control how consensus columns are defined in an alignment.

       --fast Define consensus columns as those that have a fraction >= symfrac of residues as opposed to  gaps.
              (See below for the --symfrac option.) This is the default.

       --hand Define  consensus  columns  in  next profile using reference annotation to the multiple alignment.
              This allows you to define any consensus columns you like.

       --symfrac <x>
              Define the residue fraction threshold necessary to define a consensus column when using the --fast
              option. The default is 0.5. The symbol fraction in each column is calculated after taking relative
              sequence weighting into account, and ignoring gap characters corresponding  to  ends  of  sequence
              fragments  (as  opposed  to  internal insertions/deletions).  Setting this to 0.0 means that every
              alignment column will be assigned as consensus, which may be useful in some cases. Setting  it  to
              1.0  means  that only columns that include 0 gaps (internal insertions/deletions) will be assigned
              as consensus.

       --fragthresh <x>
              We only want to count terminal gaps as deletions if the aligned sequence  is  known  to  be  full-
              length,  not if it is a fragment (for instance, because only part of it was sequenced). HMMER uses
              a simple rule to infer fragments: if the range of a sequence  in  the  alignment  (the  number  of
              alignment columns between the first and last positions of the sequence) is less than or equal to a
              fraction <x> times the alignment length in columns, then the sequence is handled  as  a  fragment.
              The  default  is 0.5.  Setting --fragthresh0 will define no (nonempty) sequence as a fragment; you
              might want to do this if you  know  you've  got  a  carefully  curated  alignment  of  full-length
              sequences.   Setting  --fragthresh1  will  define all sequences as fragments; you might want to do
              this if you know your alignment is entirely composed of fragments, such as translated short  reads
              in metagenomic shotgun data.

OPTIONS CONTROLLING RELATIVE WEIGHTS

       HMMER  uses  an  ad hoc sequence weighting algorithm to downweight closely related sequences and upweight
       distantly related ones. This has  the  effect  of  making  models  less  biased  by  uneven  phylogenetic
       representation.  For  example,  two identical sequences would typically each receive half the weight that
       one sequence would.  These options control which algorithm gets used.

       --wpb  Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff,  J.  Mol.  Biol.
              243:574, 1994].  This is the default.

       --wgsc Use  the  Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067,
              1994].

       --wblosum
              Use the same clustering scheme that was used to weight  data  in  calculating  BLOSUM  subsitution
              matrices  [Henikoff  and  Henikoff,  Proc.  Natl. Acad. Sci 89:10915, 1992]. Sequences are single-
              linkage clustered at an identity threshold (default 0.62; see --wid) and within each cluster of  c
              sequences, each sequence gets relative weight 1/c.

       --wnone
              No relative weights. All sequences are assigned uniform weight.

       --wid <x>
              Sets  the identity threshold used by single-linkage clustering when using --wblosum.  Invalid with
              any other weighting scheme. Default is 0.62.

OPTIONS CONTROLLING EFFECTIVE SEQUENCE NUMBER

       After relative weights are determined, they are normalized to sum to a total effective  sequence  number,
       eff_nseq.   This  number  may be the actual number of sequences in the alignment, but it is almost always
       smaller than that.  The default entropy weighting method (--eent) reduces the effective  sequence  number
       to  reduce  the  information  content  (relative entropy, or average expected score on true homologs) per
       consensus position. The target relative entropy is controlled by a two-parameter function, where the  two
       parameters are settable with --ere and --esigma.

       --eent Adjust  effective sequence number to achieve a specific relative entropy per position (see --ere).
              This is the default.

       --eclust
              Set effective sequence number to the number of single-linkage  clusters  at  a  specific  identity
              threshold  (see  --eid).  This option is not recommended; it's for experiments evaluating how much
              better --eent is.

       --enone
              Turn off effective sequence number determination and just use the actual number of sequences.  One
              reason  you  might  want  to  do  this is to try to maximize the relative entropy/position of your
              model, which may be useful for short models.

       --eset <x>
              Explicitly set the effective sequence number for all models to <x>.

       --ere <x>
              Set the minimum relative entropy/position target to <x>.  Requires --eent.  Default depends on the
              sequence  alphabet.  For protein sequences, it is 0.59 bits/position; for nucleotide sequences, it
              is 0.45 bits/position.

       --esigma <x>
              Sets the minimum relative entropy contributed by an entire model alignment, over its whole length.
              This  has  the  effect of making short models have higher relative entropy per position than --ere
              alone would give. The default is 45.0 bits.

       --eid <x>
              Sets the fractional pairwise identity cutoff used by single linkage clustering with  the  --eclust
              option. The default is 0.62.

OPTIONS CONTROLLING PRIORS

       By default, weighted counts are converted to mean posterior probability parameter estimates using mixture
       Dirichlet priors.  Default mixture Dirichlet prior parameters for protein models  and  for  nucleic  acid
       (RNA and DNA) models are built in. The following options allow you to override the default priors.

       --pnone
              Don't  use  any  priors.  Probability  parameters  will  simply be the observed frequencies, after
              relative sequence weighting.

       --plaplace
              Use a Laplace +1 prior in place of the default mixture Dirichlet prior.

OPTIONS CONTROLLING E-VALUE CALIBRATION

       The location parameters for the expected score  distributions  for  MSV  filter  scores,  Viterbi  filter
       scores, and Forward scores require three short random sequence simulations.

       --EmL <n>
              Sets  the sequence length in simulation that estimates the location parameter mu for MSV filter E-
              values. Default is 200.

       --EmN <n>
              Sets the number of sequences in simulation that estimates the location parameter mu for MSV filter
              E-values. Default is 200.

       --EvL <n>
              Sets the sequence length in simulation that estimates the location parameter mu for Viterbi filter
              E-values. Default is 200.

       --EvN <n>
              Sets the number of sequences in simulation that estimates the location parameter  mu  for  Viterbi
              filter E-values. Default is 200.

       --EfL <n>
              Sets  the  sequence  length in simulation that estimates the location parameter tau for Forward E-
              values. Default is 100.

       --EfN <n>
              Sets the number of sequences in simulation that estimates the location parameter tau  for  Forward
              E-values. Default is 200.

       --Eft <x>
              Sets the tail mass fraction to fit in the simulation that estimates the location parameter tau for
              Forward evalues. Default is 0.04.

OTHER OPTIONS

       --cpu <n>
              Set the number of parallel worker threads to <n>.  By default, HMMER sets this to  the  number  of
              CPU  cores  it  detects  in your machine - that is, it tries to maximize the use of your available
              processor cores. Setting <n> higher than the number of available cores is of little if any  value,
              but  you  may  want  to  set  it to something less. You can also control this number by setting an
              environment variable, HMMER_NCPU.

              This option is only available if HMMER was compiled  with  POSIX  threads  support.  This  is  the
              default, but it may have been turned off for your site or machine for some reason.

       --informat <s>
              Declare  that  the  input  msafile  is  in  format <s>.  Currently the accepted multiple alignment
              sequence file formats include Stockholm, Aligned FASTA, Clustal, NCBI  PSI-BLAST,  PHYLIP,  Selex,
              and UCSC SAM A2M. Default is to autodetect the format of the file.

       --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 seed is 42.

       --w_beta <x>
              Window length tail mass.  The upper bound, W, on the length at which nhmmer  expects  to  find  an
              instance  of  the model is set such that the fraction of all sequences generated by the model with
              length >= W is less than <x>.  The default is 1e-7.

       --w_length <n>
              Override the model instance length upper bound, W, which is otherwise controlled by --w_beta.   It
              should  be larger than the model length. The value of W is used deep in the acceleration pipeline,
              and modest changes are not expected to impact results (though larger values of W do lead to longer
              run time).

       --mpi  Run  as  a parallel MPI program. Each alignment is assigned to a MPI worker node for construction.
              (Therefore, the maximum parallelization cannot exceed  the  number  of  alignments  in  the  input
              msafile.)   This is useful when building large profile libraries. This option is only available if
              optional MPI capability was enabled at compile-time.

       --stall
              For debugging MPI parallelization: arrest program execution immediately after start, and wait  for
              a debugger to attach to the running process and release the arrest.

       --maxinsertlen <n>
              Restrict  insert  length parameterization such that the expected insert length at each position of
              the model is no more than <n>.

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 HMMER distribution (Userguide.pdf); or
       see the HMMER web page ().

       Copyright (C) 2015 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page ().

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org