MSA scoring tools/scripts

Question

[Joe]

Does anyone know of any tools/scripts that would score a MSA in a sliding window manner?

I want to get the average identity across the length of an operon MSA, so I'm looking for something that gives me back a measure of conservation that I can graph.

I found some old threads on BioStars, but a lot of the linked packages either aren't exactly what I'm looking for, or the links etc are just defunct.

If I have to write this myself (probably with python), does anyone have any thoughts on appropriate ways to score each window?

[Benn]

Would Shannon entropy plot be helpful?

Just a thought.

Entropy From A Multiple Sequence Alignment With Gaps

[Joe]

Link looks helpful, thanks. Interesting idea to quantify the uncertainty instead of the conservation. Kinda the inverse of my initial thought process but would show the same end result I think.

Answer 1

[Joe]

Wrote my own in the end. Uses some bits of code I found online, but a bit more performant.