1hmmalign(1) HMMER Manual hmmalign(1)
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6 hmmalign - align sequences to a profile HMM
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10 hmmalign [options] <hmmfile> <seqfile>
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14 Perform a multiple sequence alignment of all the sequences in seqfile,
15 by aligning them individually to the profile HMM in hmmfile.
16 The new alignment is output to stdout in Stockholm format.
19 The sequences in seqfile are aligned in unihit local alignment mode.
23 Therefore they should already be known to contain a single domain; they
24 should not contain more than one domain. They may be fragments. The
25 optimal alignment may assign some residues as nonhomologous (N and C
26 states), in which case these residues are still included in the result‐
27 ing alignment, but shoved to the outer edges. To trim these nonhomolo‐
28 gous residues from the result, see the --trim option.
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33 -h Help; print a brief reminder of command line usage and all
34 available options.
35 -o <f> Direct the output alignment to file <f>, rather than to stdout.
38 --allcol
41 Include columns in the output alignment for every match (consen‐
42 sus) state in the hmmfile, even if it means having all-gap col‐
43 umns. This is useful in analysis pipelines that need to be able
44 to maintain a predetermined profile HMM architecture (with an
45 unchanging number of consensus columns) through an hmmalign
46 step.
47 --mapali <f>
50 Merge the existing alignment in file <f> into the result, where
51 <f> is exactly the same alignment that was used to build the
52 model in hmmfile. This is done using a map of alignment columns
53 to consensus profile positions that is stored in the hmmfile.
54 The multiple alignment in <f> will be exactly reproduced in its
55 consensus columns (as defined by the profile), but the displayed
56 alignment in insert columns may be altered, because insertions
57 relative to a profile are considered by convention to be
58 unaligned data.
59 --trim Trim nonhomologous residues (assigned to N and C states in the
63 optimal alignments) from the resulting multiple alignment out‐
64 put.
65 --amino
68 Specify that all sequences in seqfile are proteins. By default,
69 alphabet type is autodetected from looking at the residue compo‐
70 sition.
71 --dna Specify that all sequences in seqfile are DNAs.
74 --rna Specify that all sequences in seqfile are RNAs.
77 --informat <s>
80 Declare that the input seqfile is in format <s>. Accepted
81 sequence file formats include FASTA, EMBL, Genbank, DDBJ,
82 Uniprot, Stockholm, and SELEX. Default is to autodetect the for‐
83 mat of the file.
84 --outformat <s>
87 Specify that the msafile is in format <s>. Currently the
88 accepted multiple alignment sequence file formats only include
89 Stockholm and SELEX. Default is to autodetect the format of the
90 file.
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96 See hmmer(1) for a master man page with a list of all the individual
97 man pages for programs in the HMMER package.
98 For complete documentation, see the user guide that came with your
101 HMMER distribution (Userguide.pdf); or see the HMMER web page
102 (@HMMER_URL@).
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108 @HMMER_COPYRIGHT@
109 @HMMER_LICENSE@
110 For additional information on copyright and licensing, see the file
112 called COPYRIGHT in your HMMER source distribution, or see the HMMER
113 web page (@HMMER_URL@).
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118 Eddy/Rivas Laboratory
119 Janelia Farm Research Campus
120 19700 Helix Drive
121 Ashburn VA 20147 USA
122 http://eddylab.org
123HMMER @HMMER_VERSION@ @HMMER_DATE@ hmmalign(1)