hmmalign(1)							   HMMER Manual 						       hmmalign(1)

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  sequences  in  seqfile are aligned in unihit local alignment mode.	Therefore they should already be known to contain a single domain;
       they should not contain more than one domain.  They may be fragments.  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
       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.

       --allcol
	      Include columns in the output alignment for every match (consensus) state in the hmmfile, even if it means having  all-gap  columns.
	      This  is	useful in analysis pipelines that need to be able to maintain a predetermined profile HMM architecture (with an unchanging
	      number of consensus columns) through an hmmalign step.

       --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 multi-
	      ple 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 composi-
	      tion.

       --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, Stock-
	      holm, and SELEX. Default is to autodetect the format of the file.

       --outformat <s>
	      Specify  that  the msafile is in format <s>.  Currently the accepted multiple alignment sequence file formats only include Stockholm
	      and SELEX. Default is to autodetect the format of the file.

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
       (@HMMER_URL@).

COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For  additional	information  on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER 
@HMMER_VERSION@						   @HMMER_DATE@ 						       hmmalign(1)