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hmmalign(1)			 HMMER Manual			   hmmalign(1)

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 un-
	      aligned data.

       --trim Trim nonhomologous residues (assigned to N and C states  in  the
	      optimal  alignments)  from the resulting multiple	alignment out-
	      put.

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

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

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

       --informat _s_
	      Assert that input	seqfile	is in format _s_, bypassing format au-
	      todetection.  Common choices for _s_ include: fasta, embl,  gen-
	      bank.   Alignment	 formats  also	work;  common choices include:
	      stockholm, a2m, afa, psiblast, clustal, phylip.  For more	infor-
	      mation,  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).  De-
	      fault 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 HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-
       mer.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

HMMER 3.3			   Nov 2019			   hmmalign(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT | AUTHOR

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