hmmalign(1) HMMER Manual hmmalign(1)NAMEhmmalign - align sequences to a profile HMM
SYNOPSIShmmalign [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 result‐
ing alignment, but shoved to the outer edges. To trim these nonhomolo‐
gous 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 (consen‐
sus) state in the hmmfile, even if it means having all-gap col‐
umns. 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 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
unaligned data.
--trim Trim nonhomologous residues (assigned to N and C states in the
optimal alignments) from the resulting multiple alignment out‐
put.
--amino
Specify that all sequences in seqfile are proteins. By default,
alphabet type is autodetected from looking at the residue compo‐
sition.
--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, Stockholm, and SELEX. Default is to autodetect the for‐
mat 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)
