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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)

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hmmpress(1)							   HMMER Manual 						       hmmpress(1)

NAME
hmmpress - prepare an HMM database for hmmscan SYNOPSIS
hmmpress [options] <hmmfile> DESCRIPTION
Starting from a profile database <hmmfile> in standard HMMER3 format, construct binary compressed datafiles for hmmscan. The hmmpress step is required for hmmscan to work. Four files are created: <hmmfile>.h3m, <hmmfile>.h3i, <hmmfile>.h3f, and <hmmfile>.h3p. The <hmmfile>.h3m file contains the profile HMMs and their annotation in a binary format. The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file con- tains precomputed data structures for the fast heuristic filter (the MSV filter). The <hmmfile>.h3p file contains precomputed data struc- tures for the rest of each profile. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. -f Force; overwrites any previous hmmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first. 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@ hmmpress(1)
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