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CLC Gene Workbench is a software suite with a range of advanced and integrated DNA sequence analysis tools - among others, assembly of DNA sequence data, advanced primer design, and molecular cloning. Available for Windows, Mac OS X, and Linux.
http://www.clcbio.com/index.php?id=27

CloneIt! - An ANSI-C program finding sub-cloning strategies, in-frame deletions and frameshifts using restriction enzymes and DNA polymerases.
http://locus.jouy.inra.fr/soft/cloneit/cloneit.html