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CloneMap provides a complete solution for fast and easy plasmid map drawing,restriction site mapping, and virtural cloning.
http://www.cgcsci.com/#CloneMap

AcaClone pDRAW32 - Freeware DNA cloning, analysis and plasmid/DNA plotting software.
http://www.acaclone.com/

AiO - All in One. DNA/protein programs and oligonucleotide databases combined in one package.
http://134.99.88.55/aio/

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

Clone Manager 5 for Windows 95 -- Software to handle enzyme operations, cloning simulation, graphic map drawing.
http://www.scied.com/ses_cm5.htm

DNASIS - genetic systems: plasmid map drawing, primer design, multiple sequence alignment etc. .
http://www.oligo.net/dnasis.htm

Redasoft Plasmid 1.0 is a software tool designed to help you create and publish high quality vector maps and perform DNA sequence analysis.
http://www.redasoft.com/

Vector NTI Suite is a comprehensive software package for computer support of molecular biology and genetics
http://www.informaxinc.com/products/vntisuite/index.html