Provided by: hmmer_3.1b1-3_amd64 
NAME
phmmer - search protein sequence(s) against a protein sequence database
SYNOPSIS
phmmer [options] <seqfile> <seqdb>
DESCRIPTION
phmmer is used to search one or more query protein sequences against a protein sequence
database. For each query sequence in <seqfile>, use that sequence to search the target
database of sequences in <seqdb>, and output ranked lists of the sequences with the most
significant matches to the query.
Either the query <seqfile> or the target <seqdb> may be '-' (a dash character), in which
case the query sequences or target database input will be read from a <stdin> pipe instead
of from a file. Only one input source can come through <stdin>, not both. An exception is
that if the <seqfile> contains more than one query sequence, then <seqdb> cannot come from
<stdin>, because we can't rewind the streaming target database to search it with another
query.
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.
OPTIONS FOR CONTROLLING OUTPUT
-o <f> Direct the main human-readable output to a file <f> instead of the default stdout.
-A <f> Save a multiple alignment of all significant hits (those satisfying inclusion
thresholds) to the file <f> in Stockholm format.
--tblout <f>
Save a simple tabular (space-delimited) file summarizing the per-target output,
with one data line per homologous target sequence found.
--domtblout <f>
Save a simple tabular (space-delimited) file summarizing the per-domain output,
with one data line per homologous domain detected in a query sequence for each
homologous model.
--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 SCORING SYSTEM
The probability model in phmmer is constructed by inferring residue probabilities from a
standard 20x20 substitution score matrix, plus two additional parameters for position-
independent gap open and gap extend probabilities.
--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. Only one of the --mx and --mxfile options may be used.
OPTIONS CONTROLLING REPORTING THRESHOLDS
Reporting thresholds control which hits are reported in output files (the main output,
--tblout, and --domtblout). 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> In the per-target output, report target sequences with an E-value of <= <x>. The
default is 10.0, meaning that on average, about 10 false positives will be reported
per query, so you can see the top of the noise and decide for yourself if it's
really noise.
-T <x> Instead of thresholding per-profile output on E-value, instead report target
sequences with a bit score of >= <x>.
--domE <x>
In the per-domain output, for target sequences that have already satisfied the per-
profile reporting threshold, report individual domains with a conditional E-value
of <= <x>. The default is 10.0. A conditional E-value means the expected number
of additional false positive domains in the smaller search space of those
comparisons that already satisfied the per-target reporting threshold (and thus
must have at least one homologous domain already).
--domT <x>
Instead of thresholding per-domain output on E-value, instead report domains with a
bit score of >= <x>.
OPTIONS CONTROLLING INCLUSION THRESHOLDS
Inclusion thresholds are stricter than reporting thresholds. They control which hits are
included in any output multiple alignment (the -A option) and which domains are marked as
significant ("!") as opposed to questionable ("?") in domain output.
--incE <x>
Use an E-value of <= <x> as the per-target inclusion threshold. The default is
0.01, meaning that on average, about 1 false positive would be expected in every
100 searches with different query sequences.
--incT <x>
Instead of using E-values for setting the inclusion threshold, instead use a bit
score of >= <x> as the per-target inclusion threshold. By default this option is
unset.
--incdomE <x>
Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in
targets that have already satisfied the overall per-target inclusion threshold.
The default is 0.01.
--incdomT <x>
Instead of using E-values, use a bit score of >= <x> as the per-domain inclusion
threshold. By default this option is unset.
OPTIONS CONTROLLING THE ACCELERATION PIPELINE
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 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>
Declare that the input <seqfile> is in format <s>. Accepted formats include fasta,
embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, and afa. The default is to
autodetect the format of the file.
--tformat <s>
Declare that the input <seqdb> is in format <s>. Accepted formats include fasta,
embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, and afa. The default is to
autodetect the format of the file.
--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 at compile-time for your site
or machine for some reason.
--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 in MPI master/worker mode, using mpirun. (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 ().
COPYRIGHT
Copyright (C) 2013 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