Is There A Way To Calculate If Two Columns In Alignment Are Significantly Different?

Question

[microbeatic]

Given two multiple sequence alignment that have columns that correspond to each other, is there a way to calculate if the two corresponding columns are significantly different?

I am trying to distinguish between two closely related groups of homologs. I wanted to identify column/regions between two groups that are different - conserved in one and not in other - to use the column as proxy in a matrix.

[ancient_learner]

I dint understand properly can you make it more clear?

[microbeatic]

I added further explanation. Hope its clear.

Answer 1

[Ashutosh Pandey]

Google for Shannon's entropy and multiple sequence alignment.