hmmalign.man

这是一个基于HMM 模型的生物多序列比对算法的linux实现版本。hmmer

.TH "hmmalign" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"

.SH NAME
.TP 
hmmalign - align sequences to an HMM profile

.SH SYNOPSIS
.B hmmalign
.I [options]
.I hmmfile
.I seqfile

.SH DESCRIPTION

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

.PP
.I 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).

.SH OPTIONS

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

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

.TP 
.BI -o " <f>"
Save alignment to file
.I <f>
instead of to standard output.

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

.SH EXPERT OPTIONS

.TP
.BI --informat " <s>"
Assert that the input 
.I seqfile
is in format
.I <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.

.TP
.BI --mapali " <f>"
Reads an alignment from file 
.I <f>
and aligns it as a single object to the HMM; e.g. the alignment in 
.I <f> 
is held fixed. 
This allows you to align sequences to a model with 
.B 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
.I <f> 
must be exactly the alignment that the HMM was built from.
Compare the
.B --withali 
option.

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

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

.TP 
.BI --withali " <f>"
Reads an alignment from file 
.I <f>
and aligns it as a single object to the HMM; e.g. the alignment in 
.I <f> 
is held fixed.
This allows you to align sequences to a model with 
.B 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
.B --mapali 
option.


.SH SEE ALSO

Master man page, with full list of and guide to the individual man
pages: see 
.B hmmer(1).
.PP
For complete documentation, see the user guide that came with the
distribution (Userguide.pdf); or see the HMMER web page,
http://hmmer.wustl.edu/.

.SH COPYRIGHT

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

.SH AUTHOR 

.nf
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/
.fi