I agree that the price of Vector NTI is awful.
Our lab finally gave up using such commercial software,
and now switched to use "BioEdit".
Although the aim of this software focuses on sequence
alignment, most of the functions for cloning, vector
construction, restriction enzyme mapping, etc. were
supported.
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Sorry if you've known about that.
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