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hmmalign(1)                      HMMER Manual                      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

HMMER @HMMER_VERSION@            @HMMER_DATE@                      hmmalign(1)