Recombinant DNA is an important tool to study molecular mechanisms of animal/plant. Though many techniques and software have been developed to make molecular research activities easy, perfect and quick decision regarding appropriate technique selection remain still complicated.
I used to use Vector NTI as designing software. I'm out of DNA for a while now but I had very good experiences w/ it. Complete in silico cloning. It helped me with cloning around 200 vectors. I would have ran into unforeseen trouble with around 10% of them if I hadn't done the in silico design first. Free trial. Negative is that if you once start to use some software, you have to keep using (and paying) the same software. Of course one can export sequence date for use in other software, but most likely you lose information (Reading frame of GOI, antibiotics resistance et cetera). This account for all software. So keep that in mind.
Free software I used as well is pDRAW.
Also free is UGene (http://ugene.unipro.ru). It is a fairly full-featured DNA analysis suite, and goes beyond clone design.
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