-bash-3.2$ /sw/opt/hmmer3/bin/jackhmmer -h
# jackhmmer :: iteratively search a protein sequence against a protein database
# HMMER 3.0 (March 2010); http://hmmer.org/
# Copyright (C) 2010 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Usage: jackhmmer [-options] <query seqfile> <target seqdb>

where basic options are:
  -h     : show brief help on version and usage
  -N <n> : set maximum number of iterations to <n>  [5]  (n>0)

options directing output:
  -o <f>          : direct output to file <f>, not stdout
  -A <f>          : save multiple alignment of hits to file <s>
  --tblout <f>    : save parseable table of per-sequence hits to file <s>
  --domtblout <f> : save parseable table of per-domain hits to file <s>
  --chkhmm <f>    : save HMM checkpoints to files <s>-<iteration>.hmm
  --chkali <f>    : save alignment checkpoints to files <s>-<iteration>.sto
  --acc           : prefer accessions over names in output
  --noali         : don't output alignments, so output is smaller
  --notextw       : unlimit ASCII text output line width
  --textw <n>     : set max width of ASCII text output lines  [120]  (n>=120)

options controlling scoring system in first iteration:
  --popen <x>   : gap open probability  [0.02]  (0<=x<0.5)
  --pextend <x> : gap extend probability  [0.4]  (0<=x<1)
  --mxfile <f>  : substitution score matrix [default: BLOSUM62]

options controlling reporting thresholds:
  -E <x>     : report sequences <= this E-value threshold in output  [10.0]  (x>0)
  -T <x>     : report sequences >= this score threshold in output
  --domE <x> : report domains <= this E-value threshold in output  [10.0]  (x>0)
  --domT <x> : report domains >= this score cutoff in output

options controlling significance thresholds for inclusion in next round:
  --incE <x>    : consider sequences <= this E-value threshold as significant
  --incT <x>    : consider sequences >= this score threshold as significant
  --incdomE <x> : consider domains <= this E-value threshold as significant
  --incdomT <x> : consider domains >= this score threshold as significant

options controlling acceleration heuristics:
  --max    : Turn all heuristic filters off (less speed, more power)
  --F1 <x> : Stage 1 (MSV) threshold: promote hits w/ P <= F1  [0.02]
  --F2 <x> : Stage 2 (Vit) threshold: promote hits w/ P <= F2  [1e-3]
  --F3 <x> : Stage 3 (Fwd) threshold: promote hits w/ P <= F3  [1e-5]
  --nobias : turn off composition bias filter

options controlling model construction after first iteration:
  --fast           : assign cols w/ >= symfrac residues as consensus
  --hand           : manual construction (requires reference annotation)
  --symfrac <x>    : sets sym fraction controlling --fast construction
  --fragthresh <x> : if L < x<L>, tag sequence as a fragment

options controlling relative weights in models after first iteration:
  --wpb     : Henikoff position-based weights  [default]
  --wgsc    : Gerstein/Sonnhammer/Chothia tree weights
  --wblosum : Henikoff simple filter weights
  --wnone   : don't do any relative weighting; set all to 1
  --wid <x> : for --wblosum: set identity cutoff  [0.62]  (0<=x<=1)

options controlling effective seq number in models after first iteration:
  --eent       : adjust eff seq # to achieve relative entropy target  [default]
  --eclust     : eff seq # is # of single linkage clusters
  --enone      : no effective seq # weighting: just use nseq
  --eset <x>   : set eff seq # for all models to <x>
  --ere <x>    : for --eent: set minimum rel entropy/position to <x>
  --esigma <x> : for --eent: set sigma param to <x>  [45.0]
  --eid <x>    : for --eclust: set fractional identity cutoff to <x>  [0.62]

Options controlling E value calibration:
  --EmL <n> : length of sequences for MSV Gumbel mu fit  [200]  (n>0)
  --EmN <n> : number of sequences for MSV Gumbel mu fit  [200]  (n>0)
  --EvL <n> : length of sequences for Viterbi Gumbel mu fit  [200]  (n>0)
  --EvN <n> : number of sequences for Viterbi Gumbel mu fit  [200]  (n>0)
  --EfL <n> : length of sequences for Forward exp tail tau fit  [100]  (n>0)
  --EfN <n> : number of sequences for Forward exp tail tau fit  [200]  (n>0)
  --Eft <x> : tail mass for Forward exponential tail tau fit  [0.04]  (0<x<1)

Other expert options:
  --nonull2     : turn off biased composition score corrections
  -Z <x>        : set # of comparisons done, for E-value calculation
  --domZ <x>    : set # of significant seqs, for domain E-value calculation
  --seed <n>    : set RNG seed to <n> (if 0: one-time arbitrary seed)  [42]
  --qformat <s> : assert query <seqfile> is in format <s>: no autodetection
  --tformat <s> : assert target <seqdb> is in format <s>>: no autodetection
  --cpu <n>     : number of parallel CPU workers to use for multithreads