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There is nothign wrong in running commercial software in linux. Linux is free as free speech, not free as free beer. Which means is compatible with comercial software, it just doesn't share the same philosofy.
On the other hand, I REALLY suggest the OP to try https://www.sagemath.org/
It's a very good replacement for matlab, and everything you learn while using it can also be used to program your own programs and commands because it uses python as a background.