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) 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

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