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) 2023 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

HMMER 3.4                                           Aug 2023                                         hmmalign(1)