1esl-alirev(1) Easel Manual esl-alirev(1)
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6 esl-alirev - reverse complement a multiple alignment
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11 esl-alirev [options] msafile
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16 esl-alirev reads the multiple alignment in msafile and outputs its re‐
17 verse complement to stdout.
18 An example of where you might need to do this is when you've downloaded
21 a chunk of multiway genomic alignment from one of the genome browsers,
22 but your RNA of interest is on the opposite strand.
23 Any per-column and per-residue annotation lines are reversed as well,
26 including Stockholm format and old SELEX format annotations. Annota‐
27 tions that Easel recognizes as secondary structure annotation (a con‐
28 sensus structure line, individual secondary structure lines) will be
29 "reverse complemented" to preserve proper bracketing orders: for exam‐
30 ple, ...<<<...>>> is reverse complemented to <<<...>>>..., not simply
31 reversed to >>>...<<<..., which would be wrong.
32 If msafile is - (a single dash), alignment input is read from stdin.
35 By default the output alignment is written in the same format as the
39 input alignment. See the --outformat option to use a different output
40 format.
41 Because the alignment is parsed into Easel's digital internal represen‐
44 tation, the output alignment may differ in certain details from the
45 original alignment; these details should be inconsequential but may
46 catch your eye. One is that if you have a reference annotation line,
47 Easel's output will put consensus residues in upper case, nonconsensus
48 (inserted) residues in lower case. Another is that the headers for some
49 formats, such as Clustal format, are written with an arbitrary version
50 number - so you may find yourself revcomping an alignment in "MUSCLE
51 (3.7) multiple sequence alignment" format and it could come out claim‐
52 ing to be a "CLUSTAL 2.1 multiple sequence alignment", just because
53 Easel writes all of its Clustal format alignment files with that
54 header.
55 The msafile must contain nucleic acid sequences (DNA or RNA). The al‐
58 phabet will be autodetected by default. See the --dna or --rna options
59 to assert an alphabet.
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65 -h Print brief help; includes version number and summary of all
66 options, including expert options.
67 --informat <s>
70 Assert that input msafile is in alignment format <s>, bypassing
71 format autodetection. Common choices for <s> include: stock‐
72 holm, a2m, afa, psiblast, clustal, phylip. For more informa‐
73 tion, and for codes for some less common formats, see main docu‐
74 mentation. The string <s> is case-insensitive (a2m or A2M both
75 work).
76 --outformat <s>
79 Write the output alignment in alignment format <s>. Common
80 choices for <s> include: stockholm, a2m, afa, psiblast, clustal,
81 phylip. The string <s> is case-insensitive (a2m or A2M both
82 work). Default is to use same format as the input msafile.
83 --dna Assert that the msafile contains DNA sequences.
86 --rna Assert that the msafile contains RNA sequences.
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93 http://bioeasel.org/
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97 Copyright (C) 2020 Howard Hughes Medical Institute.
98 Freely distributed under the BSD open source license.
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102 http://eddylab.org
103Easel 0.48 Nov 2020 esl-alirev(1)