hmmalign(1)

NAME
hmmalign - align sequences to a profile HMM

SYNOPSIS
hmmalign [options] <hmmfile> <seqfile>

DESCRIPTION

Perform a multiple sequence alignment of all the sequences in seqfile, by aligning them individually to the profile HMM in hmmfile.

The new alignment is output to stdout in Stockholm format.

The sequences in seqfile are aligned in unihit local alignment mode. Therefore they should already be known to contain a single domain; they should not contain more than one domain. They may be fragments. The optimal alignment may assign some residues as nonhomologous (N and C states), in which case these residues are still included in the resulting alignment, but shoved to the outer edges. To trim these nonhomologous residues from the result, see the --trim option.

OPTIONS

-h  Help; print a brief reminder of command line usage and all available options.

-o <f>
    Direct the output alignment to file <f>, rather than to stdout.

--allcol
    Include columns in the output alignment for every match (consensus) state in the hmmfile, even if it means having all-gap columns. This is useful in analysis pipelines that need to be able to maintain a predetermined profile HMM architecture (with an unchanging number of consensus columns) through an hmmalign step.

--mapali <f>
    Merge the existing alignment in file <f> into the result, where <f> is exactly the same alignment that was used to build the model in hmmfile. This is done using a map of alignment columns to consensus profile positions that is stored in the hmmfile. The multiple alignment in <f> will be exactly reproduced in its consensus columns (as defined by the profile), but the displayed alignment in insert columns may be altered, because insertions relative to a profile are considered by convention to be unaligned data.

--trim
    Trim nonhomologous residues (assigned to N and C states in the optimal alignments) from the resulting multiple alignment output.

--amino
    Specify that all sequences in seqfile are proteins. By default, alphabet type is autodetected from looking at the residue composition.

--dna
    Specify that all sequences in seqfile are DNAs.

--rna
    Specify that all sequences in seqfile are RNAs.

--informat <s>
    Declare that the input seqfile is in format <s>. Accepted sequence file formats include FASTA, EMBL, Genbank, DDBJ, Uniprot, Stockholm, and SELEX. Default is to autodetect the format of the file.

--outformat <s>
    Specify that the msafile is in format <s>. Currently the accepted multiple alignment sequence file formats only include Stockholm and SELEX. Default is to autodetect the format of the file.

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 (@HMMER_URL@).

COPYRIGHT
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@).

AUTHOR
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org