NAME¶
hmmbuild - construct profile HMM(s) from multiple sequence alignment(s)
SYNOPSIS¶
hmmbuild [options] <hmmfile_out>
<msafile>
DESCRIPTION¶
For each multiple sequence alignment in
<msafile> build a profile
HMM and save it to a new file
<hmmfile_out>.
<msafile> may be '-' (dash), which means reading this input from
stdin rather than a file. To use '-', you must also specify the
alignment file format with
--informat <s>, as in
--informat stockholm (because of a current limitation in our
implementation, MSA file formats cannot be autodetected in a nonrewindable
input stream.)
<hmmfile_out> may not be '-'
(stdout), because sending the
HMM file to
stdout would conflict with the other text output of the
program.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all available
options.
- -n <s>
- Name the new profile <s>. The default is to use the name of
the alignment (if one is present in the msafile, or, failing that,
the name of the hmmfile. If msafile contains more than one
alignment, -n doesn't work, and every alignment must have a name
annotated in the msafile (as in Stockholm #=GF ID annotation).
- -o <f>
- Direct the summary output to file <f>, rather than to
stdout.
- -O <f>
- After each model is constructed, resave annotated, possibly modified
source alignments to a file <f> in Stockholm format. The
alignments are annotated with a reference annotation line indicating which
columns were assigned as consensus, and sequences are annotated with what
relative sequence weights were assigned. Some residues of the alignment
may have been shifted to accommodate restrictions of the Plan7 profile
architecture, which disallows transitions between insert and delete
states.
OPTIONS FOR SPECIFYING THE ALPHABET¶
The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at
the composition of the
msafile. Autodetection is normally quite
reliable, but occasionally alphabet type may be ambiguous and autodetection
can fail (for instance, on tiny toy alignments of just a few residues). To
avoid this, or to increase robustness in automated analysis pipelines, you may
specify the alphabet type of
msafile with these options.
- --amino
- Specify that all sequences in msafile are proteins.
- --dna
- Specify that all sequences in msafile are DNAs.
- --rna
- Specify that all sequences in msafile are RNAs.
OPTIONS CONTROLLING PROFILE CONSTRUCTION¶
These options control how consensus columns are defined in an alignment.
- --fast
- Define consensus columns as those that have a fraction >=
symfrac of residues as opposed to gaps. (See below for the
--symfrac option.) This is the default.
- --hand
- Define consensus columns in next profile using reference annotation to the
multiple alignment. This allows you to define any consensus columns you
like.
- --symfrac <x>
- Define the residue fraction threshold necessary to define a consensus
column when using the --fast option. The default is 0.5. The symbol
fraction in each column is calculated after taking relative sequence
weighting into account, and ignoring gap characters corresponding to ends
of sequence fragments (as opposed to internal insertions/deletions).
Setting this to 0.0 means that every alignment column will be assigned as
consensus, which may be useful in some cases. Setting it to 1.0 means that
only columns that include 0 gaps (internal insertions/deletions) will be
assigned as consensus.
- --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
--fragthresh0 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
--fragthresh1 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¶
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. 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; for nucleotide sequences, it
is 0.45 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¶
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¶
The location parameters for the expected score distributions for MSV filter
scores, Viterbi filter scores, and Forward scores require 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¶
- --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 for your
site or machine for some reason.
- --informat <s>
- Declare that the input msafile is in format <s>.
Currently the accepted multiple alignment sequence file formats include
Stockholm, Aligned FASTA, Clustal, NCBI PSI-BLAST, PHYLIP, Selex, and UCSC
SAM A2M. Default is to autodetect the format of the file.
- --seed <n>
- Seed the random number generator with <n>, an integer >=
0. If <n> is nonzero, 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.
- --w_beta <x>
- Window length tail mass. The upper bound, W, on the length at which
nhmmer expects to find an instance of the model is set such that the
fraction of all sequences generated by the model with length >=
W is less than <x>. The default is 1e-7.
- --w_length <n>
- Override the model instance length upper bound, W, which is
otherwise controlled by --w_beta. It should be larger than the
model length. The value of W is used deep in the acceleration
pipeline, and modest changes are not expected to impact results (though
larger values of W do lead to longer run time).
- --mpi
- Run as a parallel MPI program. Each alignment is assigned to a MPI worker
node for construction. (Therefore, the maximum parallelization cannot
exceed the number of alignments in the input msafile.) This is
useful when building large profile libraries. This option is only
available if optional MPI capability was enabled at compile-time.
- --stall
- For debugging MPI parallelization: arrest program execution immediately
after start, and wait for a debugger to attach to the running process and
release the arrest.
- --maxinsertlen <n>
- Restrict insert length parameterization such that the expected insert
length at each position of the model is no more than <n>.
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