Negative entropy?

[multimeric]

Just noticing that your formula for entropy doesn't have the negative sign: https://github.com/benhid/pyMSA/blob/570d902bbc214a30f18b93adf735c46836611bf5/pymsa/core/score.py#L84

So an MSA that is high entropy (ie very random) will appear as a large negative number, which is a bit confusing, when instead it should be a large positive number.

[multimeric]

I guess the justification is that, you normally want scores to be high when the alignment is good, while entropy is high when the alignment is bad. So you have taken the negative of it in order to behave like the other metrics. Still it might be good if this were documented.