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