GENtle is a free molecular biology software for editing DNA and amino acids, database management, plasmid maps, simulation of DNA ligation and digestion with restriction enzymes, sequence aligning tool, sequencer data import, calculators, PCR tool for primer design, protein tool and so on. GENtle has even a virtual gel display so you know in advance how your gel should look in the end.
It is free software under GPLv2+.
GENtle is available for Windows, Mac and Linux.