How do I generate a character state matrix?
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.
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mdsiddra •
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Why don't you want to use tools, and reinvent the wheel? Is this a home work assignment?
Yes , this is my assignment . I have to write codes doing this myself and my problem is that I am not getting the logic how to consider the amino acids as characters and generating a matrix.
I have a aligned protein sequence file and I want to generate a character based matrix and calculate maximum likelihood for the data. The problem is that I am not getting the way how do I do it?
Hello mdsiddra!
Questions similar to yours can already be found at:
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Cheers!
PS: Please do not post duplicate questions that appear to contain very similar questions.
The question you have mentioned is different from my concern. I want to understand how do I consider the amino acids as character sites and produce a matrix so that a phylogenetic tree can further be constructed from those values.