.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
