Provided by: hmmer_3.1b2-2_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) 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