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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 package called "psutils" available on most Linux archives, that contains various Postscript tools. These include "psnup" which lets you print multiple pages on one sheet of paper with more flexibility than Mup's panelsperpage parameter, and "psselect" which prints a subset of pages.
You can check the user donated programs page on Arkkra's web site for other programs for processing Mup input or output.