1hmmalign(1) HMMER Manual hmmalign(1)
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6 hmmalign - align sequences to an HMM profile
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10 hmmalign [options] hmmfile seqfile
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14 hmmalign reads an HMM file from hmmfile and a set of sequences from
15 seqfile, aligns the sequences to the profile HMM, and outputs a multi‐
16 ple sequence alignment.
17 seqfile may be in any unaligned or aligned file format accepted by
20 HMMER. If it is in a multiple alignment format (e.g. Stockholm, MSF,
21 SELEX, ClustalW), the existing alignment is ignored (i.e., the
22 sequences are read as if they were unaligned - hmmalign will align them
23 the way it wants).
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27 -h Print brief help; includes version number and summary of all
28 options, including expert options.
29 -m Include in the alignment only those symbols aligned to match
32 states. Do not show symbols assigned to insert states.
33 -o <f> Save alignment to file <f> instead of to standard output.
36 -q quiet; suppress all output except the alignment itself. Useful
39 for piping or redirecting the output.
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43 --informat <s>
44 Assert that the input seqfile is in format <s>; do not run
45 Babelfish format autodection. This increases the reliability of
46 the program somewhat, because the Babelfish can make mistakes;
47 particularly recommended for unattended, high-throughput runs of
48 HMMER. Valid format strings include FASTA, GENBANK, EMBL, GCG,
49 PIR, STOCKHOLM, SELEX, MSF, CLUSTAL, and PHYLIP. See the User's
50 Guide for a complete list.
51 --mapali <f>
54 Reads an alignment from file <f> and aligns it as a single
55 object to the HMM; e.g. the alignment in <f> is held fixed.
56 This allows you to align sequences to a model with hmmalign and
57 view them in the context of an existing trusted multiple align‐
58 ment. The alignment to the alignment is defined by a "map" kept
59 in the HMM, and so is fast and guaranteed to be consistent with
60 the way the HMM was constructed from the alignment. The align‐
61 ment in the file <f> must be exactly the alignment that the HMM
62 was built from. Compare the --withali option.
63 --oneline
66 Output the alignment with one line per sequence, rather than
67 interleaving the sequence alignment blocks. Only affects Stock‐
68 holm format output.
69 --outformat <s>
72 Output the alignment in format <s>. The default is Stockholm
73 format. Valid formats include Stockholm, SELEX, MSF, Clustal,
74 Phylip, and A2M.
75 --withali <f>
78 Reads an alignment from file <f> and aligns it as a single
79 object to the HMM; e.g. the alignment in <f> is held fixed.
80 This allows you to align sequences to a model with hmmalign and
81 view them in the context of an existing trusted multiple align‐
82 ment. The alignment to the alignment is done with a heuristic
83 (nonoptimal) dynamic programming procedure, which may be some‐
84 what slow and is not guaranteed to be completely consistent with
85 the way the HMM was constructed (though it should be quite
86 close). However, any alignment can be used, not just the align‐
87 ment that the HMM was built from. Compare the --mapali option.
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92 Master man page, with full list of and guide to the individual man
93 pages: see hmmer(1).
94 For complete documentation, see the user guide that came with the dis‐
96 tribution (Userguide.pdf); or see the HMMER web page,
97 http://hmmer.wustl.edu/.
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101 Copyright (C) 1992-2003 HHMI/Washington University School of Medicine.
102 Freely distributed under the GNU General Public License (GPL).
103 See the file COPYING in your distribution for details on redistribution
104 conditions.
105
108 Sean Eddy
109 HHMI/Dept. of Genetics
110 Washington Univ. School of Medicine
111 4566 Scott Ave.
112 St Louis, MO 63110 USA
113 http://www.genetics.wustl.edu/eddy/
114HMMER 2.3.2 Oct 2003 hmmalign(1)