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I’ll bite. neat ascii protein viewer
Maybe it would help you to look at the galaxy project: GitHub main site
But for big programs, ones written in C++? Good luck it won’t be easy at all. You might try wxwidgets or qt. I do not predict trying to click box-ify complex cli tools yielding much success.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.