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