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 <hmmfile> should contain only a single profile. If it contains more, only the first  profile  in  the
       file will be used.

       Either <hmmfile> or <seqfile> (but not both) may be '-' (dash), which means reading this input from stdin
       rather than a file.

       The  sequences in <seqfile> are aligned in unihit local alignment mode.  Therefore they should already be
       known to contain only a single domain (or a fragment of one).  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 unaligned 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.

       --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 output multiple alignment is in format  <s>.   Currently  the  accepted  multiple
              alignment sequence file formats only include Stockholm and SELEX.

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

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

HMMER 3.1b2                                       February 2015                                      hmmalign(1)