+++ /dev/null
--bash-3.2$ /sw/opt/hmmer3/bin/jackhmmer -h\r
-# jackhmmer :: iteratively search a protein sequence against a protein database\r
-# HMMER 3.0 (March 2010); http://hmmer.org/\r
-# Copyright (C) 2010 Howard Hughes Medical Institute.\r
-# Freely distributed under the GNU General Public License (GPLv3).\r
-# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\r
-Usage: jackhmmer [-options] <query seqfile> <target seqdb>\r
-\r
-where basic options are:\r
- -h : show brief help on version and usage\r
- -N <n> : set maximum number of iterations to <n> [5] (n>0)\r
-\r
-options directing output:\r
- -o <f> : direct output to file <f>, not stdout\r
- -A <f> : save multiple alignment of hits to file <s>\r
- --tblout <f> : save parseable table of per-sequence hits to file <s>\r
- --domtblout <f> : save parseable table of per-domain hits to file <s>\r
- --chkhmm <f> : save HMM checkpoints to files <s>-<iteration>.hmm\r
- --chkali <f> : save alignment checkpoints to files <s>-<iteration>.sto\r
- --acc : prefer accessions over names in output\r
- --noali : don't output alignments, so output is smaller\r
- --notextw : unlimit ASCII text output line width\r
- --textw <n> : set max width of ASCII text output lines [120] (n>=120)\r
-\r
-options controlling scoring system in first iteration:\r
- --popen <x> : gap open probability [0.02] (0<=x<0.5)\r
- --pextend <x> : gap extend probability [0.4] (0<=x<1)\r
- --mxfile <f> : substitution score matrix [default: BLOSUM62]\r
-\r
-options controlling reporting thresholds:\r
- -E <x> : report sequences <= this E-value threshold in output [10.0] (x>0)\r
- -T <x> : report sequences >= this score threshold in output\r
- --domE <x> : report domains <= this E-value threshold in output [10.0] (x>0)\r
- --domT <x> : report domains >= this score cutoff in output\r
-\r
-options controlling significance thresholds for inclusion in next round:\r
- --incE <x> : consider sequences <= this E-value threshold as significant\r
- --incT <x> : consider sequences >= this score threshold as significant\r
- --incdomE <x> : consider domains <= this E-value threshold as significant\r
- --incdomT <x> : consider domains >= this score threshold as significant\r
-\r
-options controlling acceleration heuristics:\r
- --max : Turn all heuristic filters off (less speed, more power)\r
- --F1 <x> : Stage 1 (MSV) threshold: promote hits w/ P <= F1 [0.02]\r
- --F2 <x> : Stage 2 (Vit) threshold: promote hits w/ P <= F2 [1e-3]\r
- --F3 <x> : Stage 3 (Fwd) threshold: promote hits w/ P <= F3 [1e-5]\r
- --nobias : turn off composition bias filter\r
-\r
-options controlling model construction after first iteration:\r
- --fast : assign cols w/ >= symfrac residues as consensus\r
- --hand : manual construction (requires reference annotation)\r
- --symfrac <x> : sets sym fraction controlling --fast construction\r
- --fragthresh <x> : if L < x<L>, tag sequence as a fragment\r
-\r
-options controlling relative weights in models after first iteration:\r
- --wpb : Henikoff position-based weights [default]\r
- --wgsc : Gerstein/Sonnhammer/Chothia tree weights\r
- --wblosum : Henikoff simple filter weights\r
- --wnone : don't do any relative weighting; set all to 1\r
- --wid <x> : for --wblosum: set identity cutoff [0.62] (0<=x<=1)\r
-\r
-options controlling effective seq number in models after first iteration:\r
- --eent : adjust eff seq # to achieve relative entropy target [default]\r
- --eclust : eff seq # is # of single linkage clusters\r
- --enone : no effective seq # weighting: just use nseq\r
- --eset <x> : set eff seq # for all models to <x>\r
- --ere <x> : for --eent: set minimum rel entropy/position to <x>\r
- --esigma <x> : for --eent: set sigma param to <x> [45.0]\r
- --eid <x> : for --eclust: set fractional identity cutoff to <x> [0.62]\r
-\r
-Options controlling E value calibration:\r
- --EmL <n> : length of sequences for MSV Gumbel mu fit [200] (n>0)\r
- --EmN <n> : number of sequences for MSV Gumbel mu fit [200] (n>0)\r
- --EvL <n> : length of sequences for Viterbi Gumbel mu fit [200] (n>0)\r
- --EvN <n> : number of sequences for Viterbi Gumbel mu fit [200] (n>0)\r
- --EfL <n> : length of sequences for Forward exp tail tau fit [100] (n>0)\r
- --EfN <n> : number of sequences for Forward exp tail tau fit [200] (n>0)\r
- --Eft <x> : tail mass for Forward exponential tail tau fit [0.04] (0<x<1)\r
-\r
-Other expert options:\r
- --nonull2 : turn off biased composition score corrections\r
- -Z <x> : set # of comparisons done, for E-value calculation\r
- --domZ <x> : set # of significant seqs, for domain E-value calculation\r
- --seed <n> : set RNG seed to <n> (if 0: one-time arbitrary seed) [42]\r
- --qformat <s> : assert query <seqfile> is in format <s>: no autodetection\r
- --tformat <s> : assert target <seqdb> is in format <s>>: no autodetection\r
- --cpu <n> : number of parallel CPU workers to use for multithreads\r
git://source.jalview.org / jabaws.git / blobdiff