Off topic:How do I generate a character state matrix?

Question

[mdsiddra]

I am using Biopython for writing some codes for generating a character based matrix (for amino acids).

I have a protein alignment file and I want to use it to create a matrix using a character based method so that a phylogenetic tree can be generated from it.

My question is I don't know how to generate a character based matrix?? I somehow understand the logics for a distance based matrix but I am unable to understand the methodologies for using amino acids as characters for generating matrix. I want to write the codes for it and don't want to use any tools for this analysis.