SYNOPSIS

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 range of a sequence in the alignment (the number of alignment columns between the first and last positions of the sequence) 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>.
 

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