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Since Mup generates PostScript, almost any PostScript tool can be used on its output. In particular, the "ps2pdf" tool that comes with Ghostscript can convert Mup output to PDF format, and the "ps2epsi" tool, which also comes with Ghostscript, converts a PostScript file to an Encapsulated PostScript (EPS) file. Many text processing and graphics programs will let you import EPS files, so this can let you insert Mup output into some other document.
There is a "psutils" package, available from most Linux archives, that contains various Postscript tools. The "psnup" program lets you print multiple pages on one sheet of paper with more flexibility than Mup's panelsperpage parameter. The "psselect" command prints a subset of pages. The "psresize" command may be useful for getting something like a3 paper size, which Mup doesn't support directly via the pagesize parameter, or a size that exceeds the range of the pageheight and pagewidth parameters.
You can check the user-donated programs page on Arkkra's website for other programs for processing Mup input or output.