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>. The new
16 alignment is output to stdout in Stockholm format.
17 The <hmmfile> should contain only a single profile. If it contains
20 more, only the first profile in the file will be used.
21 Either <hmmfile> or <seqfile> (but not both) may be '-' (dash), which
24 means reading this input from stdin rather than a file.
25 The sequences in <seqfile> are aligned in unihit local alignment mode.
28 Therefore they should already be known to contain only a single domain
29 (or a fragment of one). The optimal alignment may assign some residues
30 as nonhomologous (N and C states), in which case these residues are
31 still included in the resulting alignment, but shoved to the outer
32 edges. To trim these unaligned nonhomologous residues from the result,
33 see the --trim option.
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38 -h Help; print a brief reminder of command line usage and all
39 available options.
40 -o <f> Direct the output alignment to file <f>, rather than to stdout.
43 --mapali <f>
46 Merge the existing alignment in file <f> into the result, where
47 <f> is exactly the same alignment that was used to build the
48 model in <hmmfile>. This is done using a map of alignment col‐
49 umns to consensus profile positions that is stored in the <hmm‐
50 file>. The multiple alignment in <f> will be exactly reproduced
51 in its consensus columns (as defined by the profile), but the
52 displayed alignment in insert columns may be altered, because
53 insertions relative to a profile are considered by convention to
54 be unaligned data.
55 --trim Trim nonhomologous residues (assigned to N and C states in the
59 optimal alignments) from the resulting multiple alignment out‐
60 put.
61 --amino
64 Specify that all sequences in <seqfile> are proteins. By
65 default, alphabet type is autodetected from looking at the
66 residue composition.
67 --dna Specify that all sequences in <seqfile> are DNAs.
70 --rna Specify that all sequences in <seqfile> are RNAs.
73 --informat <s>
76 Declare that the input <seqfile> is in format <s>. Accepted
77 sequence file formats include FASTA, EMBL, GenBank, DDBJ,
78 UniProt, Stockholm, and SELEX. Default is to autodetect the for‐
79 mat of the file.
80 --outformat <s>
83 Specify that the output multiple alignment is in format <s>.
84 Currently the accepted multiple alignment sequence file formats
85 only include Stockholm and SELEX.
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91 See hmmer(1) for a master man page with a list of all the individual
92 man pages for programs in the HMMER package.
93 For complete documentation, see the user guide that came with your
96 HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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102 Copyright (C) 2015 Howard Hughes Medical Institute.
103 Freely distributed under the GNU General Public License (GPLv3).
104 For additional information on copyright and licensing, see the file
106 called COPYRIGHT in your HMMER source distribution, or see the HMMER
107 web page ().
108
112 The Eddy/Rivas Laboratory
113 Janelia Farm Research Campus
114 19700 Helix Drive
115 Ashburn VA 20147 USA
116 http://eddylab.org
117HMMER 3.1b2 February 2015 hmmalign(1)