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dlthomas comments on Reforming rot13 - Less Wrong
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It's been packaged on *NIX systems forever. On Debian and Ubuntu, it's in the package "bsdgames".
Like most traditional unix utilities, it reads from stdin and writes to stdout, so if you have xclip or xsel installed you can copy the text in question, then run
xsel -ob | rot13 | xsel -ib
and then paste the rot13'ed (or un-rot13'ed) text.
You could even bind it to a key combo without too much trouble.