esl-alirev(1)

💅 esl-alirev — the Easel manual, bestie edition ✨

okay so this is esl-alirev(1), a lil tool from the Easel manual, and it does exactly one iconic thing: it reverse complements a multiple alignment. 🧬✨

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🌸 NAME 🌸

esl-alirev — reverse complement a multiple alignment 💖

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🎀 SYNOPSIS 🎀

esl-alirev [options] msafile

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🦋 DESCRIPTION 🦋

esl-alirev reads the multiple alignment in msafile and outputs its reverse complement to stdout. no cap, that's the whole vibe. 💅

An example of where you might need to do this is when you've downloaded a chunk of multiway genomic alignment from one of the genome browsers, but your RNA of interest is on the opposite strand. (the way that happens literally all the time 😭)

Any per-column and per-residue annotation lines are reversed as well, including Stockholm format and old SELEX format annotations. Annotations that Easel recognizes as secondary structure annotation (a consensus structure line, individual secondary structure lines) will be "reverse complemented" to preserve proper bracketing orders: for example, ...<<<...>>> is reverse complemented to <<<...>>>..., not simply reversed to >>>...<<<..., which would be wrong. 🫶 (like, imagine getting that wrong. not me. 🙈)

If msafile is - (a single dash), alignment input is read from stdin. 🍓

By default the output alignment is written in the same format as the input alignment. See the --outformat option to use a different output format. ✨

Because the alignment is parsed into Easel's digital internal representation, the output alignment may differ in certain details from the original alignment; these details should be inconsequential but may catch your eye. 👀 Two of them, bestie:

• One is that if you have a reference annotation line, Easel's output will put consensus residues in upper case, nonconsensus (inserted) residues in lower case.
• Another is that the headers for some formats, such as Clustal format, are written with an arbitrary version number — so you may find yourself revcomping an alignment in "MUSCLE (3.7) multiple sequence alignment" format and it could come out claiming to be a "CLUSTAL 2.1 multiple sequence alignment", just because Easel writes all of its Clustal format alignment files with that header. 💀 iconic behavior honestly.

The msafile must contain nucleic acid sequences (DNA or RNA). The alphabet will be autodetected by default. See the --dna or --rna options to assert an alphabet. 🧬

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✨ OPTIONS ✨

• -h — Print brief help; includes version number and summary of all options, including expert options. 👑 (yes bestie, the expert options are in there too)
• --informat <s> — Assert that input msafile is in alignment format <s>, bypassing format autodetection. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. For more information, and for codes for some less common formats, see main documentation. The string <s> is case-insensitive (a2m or A2M both work). 🌈
• --outformat <s> — Write the output alignment in alignment format <s>. Common choices for <s> include: stockholm, a2m, afa, psiblast, clustal, phylip. The string <s> is case-insensitive (a2m or A2M both work). Default is to use same format as the input msafile. 🎀
• --dna — Assert that the msafile contains DNA sequences. 🧬
• --rna — Assert that the msafile contains RNA sequences. 🌸

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👀 SEE ALSO 👀

http://bioeasel.org/

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💜 COPYRIGHT 💜

Copyright (C) 2020 Howard Hughes Medical Institute. Freely distributed under the BSD open source license.

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🌟 AUTHOR 🌟

http://eddylab.org

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k that's the whole page bestie, go forth and revcomp responsibly 🫶

Easel 0.48 · Nov 2020 — mwah, slay, periodt. 💅✨🌈