NAME

       hmmalign - align sequences to a profile

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.

       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
              Assert that sequences in seqfile are protein, bypassing alphabet autodetection.

       --dna  Assert that sequences in seqfile are DNA, bypassing alphabet autodetection.

       --rna  Assert that sequences in seqfile are RNA, bypassing alphabet autodetection.

       --informat <s>
              Assert that input seqfile is in format <s>, bypassing format autodetection.   Common  choices  for
              <s>  include:  fasta,  embl,  genbank.   Alignment  formats  also  work;  common  choices include:
              stockholm, a2m, afa, psiblast, clustal, phylip.  For more information, and for codes for some less
              common  formats,  see main documentation.  The string <s> is case-insensitive (fasta or FASTA both
              work).

       --outformat <s>
              Write the output alignment in format <s>.  Common choices for <s> include:  stockholm,  a2m,  afa,
              psiblast, clustal, phylip.  The string <s> is case-insensitive (a2m or A2M both work).  Default is
              stockholm.

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 (http://hmmer.org/).

COPYRIGHT

       Copyright (C) 2019 Howard Hughes Medical Institute.
       Freely distributed under the BSD open source license.

       For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
       distribution, or see the HMMER web page (http://hmmer.org/).

AUTHOR

       http://eddylab.org