http://serialbasics.free.fr/Serial_Cloner.html

I have no affiliation with them and nothing to gain. Just an honest recommendation. This program is wonderful! Handles anything VectorNTI can. Make all your constructs, in silico PCR, primer design, in silico restriction digest and ligation.

Works well for checking sequence alignment, except when checking multiple sequence files all at once. I use serial cloner to make sure the sequence is in frame if there is a tag, and then use ApE (A plasmid editor) to load all 3-5 sequence files and compare them all simultaneously.

Use this program! The senior scientists in my lab all are amazed this is offered free and that I get things done quicker than them on it VS the ridiculously overpriced NTI software.

Also donate to this developer.