Simple CLI?

[multimeric]

Hi, thanks for this wonderful library!

I'm just wondering that since we have utilities like read_fasta_file_as_list_of_pairs, and also run_all_scores which runs a comprehensive evaluation, we could write a CLI that calls these these on an input fasta alignment (and initially not support other alignment formats for simplicity), and maybe make the scores configurable via flags. It seems that there was a benchmark.py that did this (it's alluded to in the PDF), but it must have been deleted.

This would offer a very useful and easy method of evaluating MSAs, which as far as I can tell is a gap in the ecosystem at the moment.