Provided by: hmmer_3.2.1+dfsg-1_amd64 bug

NAME

       jackhmmer - iteratively search sequence(s) against a sequence database

SYNOPSIS

       jackhmmer [options] seqfile seqdb

DESCRIPTION

       jackhmmer  iteratively  searches  each  query  sequence  in  seqfile  against  the  target
       sequence(s) in seqdb.  The first iteration is identical to a phmmer search.  For the  next
       iteration, a multiple alignment of the query together with all target sequences satisfying
       inclusion thresholds is assembled, a profile is constructed from this alignment (identical
       to using hmmbuild on the alignment), and profile search of the seqdb is done (identical to
       an hmmsearch with the profile).

       The query seqfile may be '-' (a dash character), in which case  the  query  sequences  are
       read  from  a  stdin  pipe  instead of from a file.  The seqdb cannot be read from a stdin
       stream, because jackhmmer needs to do multiple passes over the database.

       The output format is designed to be  human-readable,  but  is  often  so  voluminous  that
       reading  it is impractical, and parsing it is a pain. The --tblout and --domtblout options
       save output in simple tabular formats that are concise and easier to parse.  The -o option
       allows redirecting the main output, including throwing it away in /dev/null.

OPTIONS

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

       -N <n> Set  the maximum number of iterations to <n>.  The default is 5. If N=1, the result
              is equivalent to a phmmer search.

OPTIONS CONTROLLING OUTPUT

       By default, output for each iteration appears on stdout  in  a  somewhat  human  readable,
       somewhat  parseable  format.  These  options  allow  redirecting  that  output  or  saving
       additional kinds of output to files, including checkpoint files for each iteration.

       -o <f> Direct the human-readable output to a file <f>.

       -A <f> After the final iteration,  save  an  annotated  multiple  alignment  of  all  hits
              satisfying  inclusion  thresholds  (also  including  the  original query) to <f> in
              Stockholm format.

       --tblout <f>
              After the final iteration, save a tabular summary of top sequence hits to <f> in  a
              readily parseable, columnar, whitespace-delimited format.

       --domtblout <f>
              After  the  final  iteration, save a tabular summary of top domain hits to <f> in a
              readily parseable, columnar, whitespace-delimited format.

       --chkhmm prefix
              At the start of each iteration, checkpoint the query HMM, saving it to a file named
              prefix-n.hmm where n is the iteration number (from 1..N).

       --chkali prefix
              At  the  end  of  each iteration, checkpoint an alignment of all domains satisfying
              inclusion thresholds (e.g. what will become the query HMM for the next  iteration),
              saving  it  to  a  file  named  prefix-n.sto  in  Stockholm  format, where n is the
              iteration number (from 1..N).

       --acc  Use accessions instead of names in the main output, where  available  for  profiles
              and/or sequences.

       --noali
              Omit the alignment section from the main output. This can greatly reduce the output
              volume.

       --notextw
              Unlimit the length of each line in the main output. The default is a limit  of  120
              characters  per line, which helps in displaying the output cleanly on terminals and
              in editors, but can truncate target profile description lines.

       --textw <n>
              Set the main output's line length limit to <n> characters per line. The default  is
              120.

OPTIONS CONTROLLING SINGLE SEQUENCE SCORING (FIRST ITERATION)

       By  default,  the  first  iteration  uses  a  search model constructed from a single query
       sequence. This model is constructed using a standard 20x20 substitution matrix for residue
       probabilities,  and  two  additional  parameters for position-independent gap open and gap
       extend probabilities. These options allow the default single-sequence  scoring  parameters
       to be changed.

       --popen <x>
              Set the gap open probability for a single sequence query model to <x>.  The default
              is 0.02.  <x> must be >= 0 and < 0.5.

       --pextend <x>
              Set the gap extend probability for a single  sequence  query  model  to  <x>.   The
              default is 0.4.  <x> must be >= 0 and < 1.0.

       --mx <s>
              Obtain  residue alignment probabilities from the built-in substitution matrix named
              <s>.  Several standard matrices are built-in, and do  not  need  to  be  read  from
              files.   The  matrix  name  <s>  can  be  PAM30,  PAM70,  PAM120, PAM240, BLOSUM45,
              BLOSUM50, BLOSUM62, BLOSUM80, or BLOSUM90.  Only  one  of  the  --mx  and  --mxfile
              options may be used.

       --mxfile mxfile
              Obtain residue alignment probabilities from the substitution matrix in file mxfile.
              The default score matrix is BLOSUM62 (this matrix is internal to HMMER and does not
              have to be available as a file).  The format of a substitution matrix mxfile is the
              standard format accepted by BLAST, FASTA, and  other  sequence  analysis  software.
              See ftp.ncbi.nlm.nih.gov/blast/matrices/ for example files. (The only exception: we
              require matrices to be square, so for DNA,  use  files  like  NCBI's  NUC.4.4,  not
              NUC.4.2.)

OPTIONS CONTROLLING REPORTING THRESHOLDS

       Reporting  thresholds  control  which  hits are reported in output files (the main output,
       --tblout, and --domtblout).  In each iteration, sequence hits and domain hits  are  ranked
       by  statistical significance (E-value) and output is generated in two sections called per-
       target and per-domain output. In per-target output, by default, all sequence hits with  an
       E-value <= 10 are reported. In the per-domain output, for each target that has passed per-
       target reporting thresholds, all domains satisfying per-domain  reporting  thresholds  are
       reported.  By default, these are domains with conditional E-values of <= 10. The following
       options allow you to change the default E-value reporting thresholds, or to use bit  score
       thresholds instead.

       -E <x> Report sequences with E-values <= <x> in per-sequence output. The default is 10.0.

       -T <x> Use  a  bit score threshold for per-sequence output instead of an E-value threshold
              (any setting of -E is ignored). Report sequences with a bit score of  >=  <x>.   By
              default this option is unset.

       -Z <x> Declare the total size of the database to be <x> sequences, for purposes of E-value
              calculation.  Normally E-values are calculated relative to the size of the database
              you  actually  searched  (e.g.  the  number of sequences in target_seqdb).  In some
              cases (for instance, if you've split your target sequence  database  into  multiple
              files for parallelization of your search), you may know better what the actual size
              of your search space is.

       --domE <x>
              Report domains with conditional E-values <= <x> in per-domain output,  in  addition
              to the top-scoring domain per significant sequence hit. The default is 10.0.

       --domT <x>
              Use  a  bit  score  threshold for per-domain output instead of an E-value threshold
              (any setting of --domT is ignored). Report domains with a bit score of  >=  <x>  in
              per-domain  output,  in addition to the top-scoring domain per significant sequence
              hit. By default this option is unset.

       --domZ <x>
              Declare the number of significant sequences to be <x> sequences,  for  purposes  of
              conditional  E-value  calculation  for  additional  domain  significance.  Normally
              conditional E-values are calculated relative to the  number  of  sequences  passing
              per-sequence reporting threshold.

OPTIONS CONTROLLING INCLUSION THRESHOLDS

       Inclusion thresholds control which hits are included in the multiple alignment and profile
       constructed for the next search iteration.  By  default,  a  sequence  must  have  a  per-
       sequence E-value of <= 0.001 (see -E option) to be included, and any additional domains in
       it besides the top-scoring one must have a conditional E-value of  <=  0.001  (see  --domE
       option).  The  difference  between  reporting  thresholds and inclusion thresholds is that
       inclusion thresholds control which hits actually get used in the next  iteration  (or  the
       final  output  multiple  alignment if the -A option is used), whereas reporting thresholds
       control what you see in output. Reporting thresholds are generally more loose so  you  can
       see borderline hits in the top of the noise that might be of interest.

       --incE <x>
              Include  sequences  with E-values <= <x> in subsequent iteration or final alignment
              output by -A.  The default is 0.001.

       --incT <x>
              Use a bit  score  threshold  for  per-sequence  inclusion  instead  of  an  E-value
              threshold (any setting of --incE is ignored). Include sequences with a bit score of
              >= <x>.  By default this option is unset.

       --incdomE <x>
              Include domains with conditional E-values <= <x> in subsequent iteration  or  final
              alignment  output  by  -A,  in  addition  to the top-scoring domain per significant
              sequence hit.  The default is 0.001.

       --incdomT <x>
              Use a bit score threshold for per-domain inclusion instead of an E-value  threshold
              (any setting of --incT is ignored). Include domains with a bit score of >= <x>.  By
              default this option is unset.

OPTIONS CONTROLLING ACCELERATION HEURISTICS

       HMMER3 searches are accelerated in a three-step  filter  pipeline:  the  MSV  filter,  the
       Viterbi  filter,  and  the  Forward  filter.  The  first  filter  is  the fastest and most
       approximate; the last is the full Forward scoring algorithm, slowest  but  most  accurate.
       There  is also a bias filter step between MSV and Viterbi. Targets that pass all the steps
       in the acceleration pipeline are then subjected to postprocessing -- domain identification
       and scoring using the Forward/Backward algorithm.

       Essentially  the  only  free  parameters that control HMMER's heuristic filters are the P-
       value thresholds controlling the expected fraction of nonhomologous  sequences  that  pass
       the  filters.  Setting  the  default  thresholds  higher  will pass a higher proportion of
       nonhomologous sequence, increasing  sensitivity  at  the  expense  of  speed;  conversely,
       setting  lower  P-value  thresholds will pass a smaller proportion, decreasing sensitivity
       and increasing speed. Setting a filter's P-value threshold to 1.0 means  it  will  passing
       all sequences, and effectively disables the filter.

       Changing  filter  thresholds only removes or includes targets from consideration; changing
       filter thresholds does not alter bit scores, E-values, or alignments,  all  of  which  are
       determined solely in postprocessing.

       --max  Maximum sensitivity.  Turn off all filters, including the bias filter, and run full
              Forward/Backward  postprocessing  on  every  target.  This  increases   sensitivity
              slightly, at a large cost in speed.

       --F1 <x>
              First  filter  threshold;  set  the P-value threshold for the MSV filter step.  The
              default is 0.02, meaning that roughly  2%  of  the  highest  scoring  nonhomologous
              targets are expected to pass the filter.

       --F2 <x>
              Second  filter  threshold;  set  the P-value threshold for the Viterbi filter step.
              The default is 0.001.

       --F3 <x>
              Third filter threshold; set the P-value threshold for the Forward filter step.  The
              default is 1e-5.

       --nobias
              Turn  off  the  bias filter. This increases sensitivity somewhat, but can come at a
              high cost in speed, especially if the query has biased residue composition (such as
              a  repetitive sequence region, or if it is a membrane protein with large regions of
              hydrophobicity). Without the bias filter, too many sequences may  pass  the  filter
              with   biased   queries,  leading  to  slower  than  expected  performance  as  the
              computationally intensive Forward/Backward algorithms shoulder an abnormally  heavy
              load.

OPTIONS CONTROLLING PROFILE CONSTRUCTION (LATER ITERATIONS)

       jackhmmer  always  includes  your original query sequence in the alignment result at every
       iteration, and consensus positions are always defined by that query sequence. That  is,  a
       jackhmmer  profile  is  always the same length as your original query, at every iteration.
       Therefore jackhmmer gives you less control over profile construction than  hmmbuild  does;
       it  does  not  have  the  --fast,  or  --hand,  or  --symfrac  options.   The only profile
       construction option available in jackhmmer is --fragthresh:

       --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 sequence length
              L  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
              --fragthresh  0 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  --fragthresh  1  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

       Whenever  a  profile  is  built  from  a multiple alignment, 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 (and this is why jackhmmer isn't concerned about always
       including your original query sequence in each iteration's alignment, even if it finds  it
       again in the database you're searching). 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.

       --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

       In  profile  construction,  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

       Estimating  the  location  parameters  for the expected score distributions for MSV filter
       scores, Viterbi filter scores, and Forward scores requires  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

       --nonull2
              Turn off the null2 score corrections for biased composition.

       -Z <x> Assert that the total number of targets in your searches is <x>, for  the  purposes
              of  per-sequence  E-value  calculations,  rather  than the actual number of targets
              seen.

       --domZ <x>
              Assert that the total number of targets in your searches is <x>, for  the  purposes
              of  per-domain  conditional E-value calculations, rather than the number of targets
              that passed the reporting thresholds.

       --seed <n>
              Seed the random number generator with <n>, an integer >= 0.   If  <n>  is  >0,  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.

       --qformat <s>
              Assert that input query seqfile is in format <s>, bypassing  format  autodetection.
              Common choices for <s> include: fasta, embl, genbank.  Alignment formats also work;
              common choices include: stockholm, a2m, afa, psiblast, clustal, phylip.   For  more
              information,  and  for  codes for some less common formats, see main documentation.
              The string <s> is case-insensitive (fasta or FASTA both work).

       --tformat <s>
              Assert that the input target sequence seqdb is in format <s>.  See --qformat  above
              for accepted choices for <s>.

       --cpu <n>
              Set  the  number  of  parallel  worker  threads to <n>.  On multicore machines, the
              default is 2.  You can also control this number by setting an environment variable,
              HMMER_NCPU.   There  is  also a master thread, so the actual number of threads that
              HMMER spawns is <n>+1.

              This option is not available if HMMER  was  compiled  with  POSIX  threads  support
              turned off.

       --stall
              For  debugging  the  MPI  master/worker  version:  pause after start, to enable the
              developer to attach debuggers to the running master and worker(s)  processes.  Send
              SIGCONT  signal  to  release  the  pause.   (Under gdb: (gdb) signal SIGCONT) (Only
              available if optional MPI support was enabled at compile-time.)

       --mpi  Run under  MPI  control  with  master/worker  parallelization  (using  mpirun,  for
              example,  or  equivalent).  Only  available  if optional MPI support was enabled at
              compile-time.

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 (http://hmmer.org/).

COPYRIGHT

       Copyright (C) 2018 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