calculate N-effective per site

[tijeco]

I would like to be able to add a row to the prediction columns that includes the calculated N-effective. I think this is more or less the general entropy of a given residue, or the number of possible residues that can be present there. I think of it as a proxy for diversity, if a residue has a very strong probability for one residue, low diversity, but if it has lots of low probabilities for lots of residues, high diversity!

There may be other metrics to look at, that are probably related to summarizing alignment columns.

[tijeco]

This was basically closed by 00b3700