NAME
hmmalign - align sequences to an HMM profile
SYNOPSIS
hmmalign [options] hmmfile seqfile
DESCRIPTION
hmmalign 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 - hmmalign 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 hmmalign 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 hmmalign 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 hmmer(1).
For complete documentation, see the user guide that came with the
distribution (Userguide.pdf); or see the HMMER web page,
http://hmmer.wustl.edu/.
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/