Provided by: hmmer2_2.3.2-7ubuntu1_amd64 bug

NAME

       hmm2align - align sequences to an HMM profile

SYNOPSIS

       hmm2align [options] hmm2file seqfile

DESCRIPTION

       hmm2align  reads  an HMM file from hmmfile and a set of sequences from seqfile, aligns the
       sequences to the profile HMM, and outputs a multiple sequence alignment.

       seqfile may be in any unaligned or aligned file format accepted by HMMER. If it  is  in  a
       multiple  alignment  format (e.g. Stockholm, MSF, SELEX, ClustalW), the existing alignment
       is ignored (i.e., the sequences are read as if they were unaligned - hmm2align will  align
       them the way it wants).

OPTIONS

       -h     Print  brief  help;  includes  version number and summary of all options, including
              expert options.

       -m     Include in the alignment only those symbols aligned to match states.  Do  not  show
              symbols assigned to insert states.

       -o <f> Save alignment to file <f> instead of to standard output.

       -q     quiet;  suppress  all  output  except  the  alignment itself.  Useful for piping or
              redirecting the output.

EXPERT OPTIONS

       --informat <s>
              Assert that the input seqfile is  in  format  <s>;  do  not  run  Babelfish  format
              autodection.  This  increases  the reliability of the program somewhat, because the
              Babelfish  can  make  mistakes;  particularly  recommended  for  unattended,  high-
              throughput  runs  of HMMER. Valid format strings include FASTA, GENBANK, EMBL, GCG,
              PIR, STOCKHOLM, SELEX, MSF, CLUSTAL,  and  PHYLIP.  See  the  User's  Guide  for  a
              complete list.

       --mapali <f>
              Reads  an alignment from file <f> and aligns it as a single object to the HMM; e.g.
              the alignment in <f> is held fixed.  This allows you to align sequences to a  model
              with  hmm2align  and  view  them  in  the  context  of an existing trusted multiple
              alignment.  The alignment to the alignment is defined by a "map" kept in  the  HMM,
              and so is fast and guaranteed to be consistent with the way the HMM was constructed
              from the alignment.  The alignment in the file <f> must be  exactly  the  alignment
              that the HMM was built from.  Compare the --withali option.

       --oneline
              Output  the  alignment  with  one  line  per sequence, rather than interleaving the
              sequence alignment blocks. Only affects Stockholm format output.

       --outformat <s>
              Output the alignment in format <s>.  The default is Stockholm format. Valid formats
              include Stockholm, SELEX, MSF, Clustal, Phylip, and A2M.

       --withali <f>
              Reads  an alignment from file <f> and aligns it as a single object to the HMM; e.g.
              the alignment in <f> is held fixed.  This allows you to align sequences to a  model
              with  hmm2align  and  view  them  in  the  context  of an existing trusted multiple
              alignment. The alignment to the alignment is done  with  a  heuristic  (nonoptimal)
              dynamic  programming procedure, which may be somewhat slow and is not guaranteed to
              be completely consistent with the way the HMM was constructed (though it should  be
              quite  close).  However, any alignment can be used, not just the alignment that the
              HMM was built from. Compare the --mapali option.

SEE ALSO

       Master man page, with full list of and guide to the individual man pages: see hmmer2(1).

       For        complete        documentation,        see        the         user         guide
       (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf);  or  see  the  HMMER web
       page, http://hmmer.janelia.org/.

COPYRIGHT

       Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
       Freely distributed under the GNU General Public License (GPL).
       See the file COPYING in your distribution for details on redistribution conditions.

AUTHOR

       Sean Eddy
       HHMI/Dept. of Genetics
       Washington Univ. School of Medicine
       4566 Scott Ave.
       St Louis, MO 63110 USA
       http://www.genetics.wustl.edu/eddy/