1hmmalign(1) HMMER Manual hmmalign(1)
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6 hmmalign - align sequences to a profile
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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.
17 The hmmfile should contain only a single profile. If it contains more,
20 only the first profile in the file will be used.
21 Either hmmfile or seqfile (but not both) may be '-' (dash), which means
24 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 columns
49 to consensus profile positions that is stored in the hmmfile.
50 The multiple alignment in <f> will be exactly reproduced in its
51 consensus columns (as defined by the profile), but the displayed
52 alignment in insert columns may be altered, because insertions
53 relative to a profile are considered by convention to be un‐
54 aligned 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 Assert that sequences in seqfile are protein, bypassing alphabet
65 autodetection.
66 --dna Assert that sequences in seqfile are DNA, bypassing alphabet au‐
69 todetection.
70 --rna Assert that sequences in seqfile are RNA, bypassing alphabet au‐
73 todetection.
74 --informat <s>
78 Assert that input seqfile is in format <s>, bypassing format au‐
79 todetection. Common choices for <s> include: fasta, embl, gen‐
80 bank. Alignment formats also work; common choices include:
81 stockholm, a2m, afa, psiblast, clustal, phylip. For more infor‐
82 mation, and for codes for some less common formats, see main
83 documentation. The string <s> is case-insensitive (fasta or
84 FASTA both work).
85 --outformat <s>
88 Write the output alignment in format <s>. Common choices for
89 <s> include: stockholm, a2m, afa, psiblast, clustal, phylip.
90 The string <s> is case-insensitive (a2m or A2M both work). De‐
91 fault is stockholm.
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97 See hmmer(1) for a master man page with a list of all the individual
98 man pages for programs in the HMMER package.
99 For complete documentation, see the user guide that came with your HM‐
102 MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
103 mer.org/).
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109 Copyright (C) 2020 Howard Hughes Medical Institute.
110 Freely distributed under the BSD open source license.
111 For additional information on copyright and licensing, see the file
113 called COPYRIGHT in your HMMER source distribution, or see the HMMER
114 web page (http://hmmer.org/).
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119 http://eddylab.org
120HMMER 3.3.2 Nov 2020 hmmalign(1)