I am using the pairwise2 module in biopython to do alignment and I am confusing on how to quantify the similarity of the aligned two sequences.

I have done a search of the literature and found that there is many types of similarity measure for protein alignment. For example e-value, p-value , bitscore, percentage identity, etc...

Yet which one is the most commonly used?

Thank you very much for your information. But I am not so clear with one point, in the computation of bit score it requires the parameter K and lambdam. Most of the document only mention it as a statistical parameter but didn't talk about how to compute it, do the information provided from the pairwise2 module enough to compute K and lambda or I should use another algorithm to find the bit score?

I do also find some document mentioned that K and lambda can be derived from my scoring system, does it means my score matrix?

@DK Thank you very much for your information. But I am not so clear with one point, in the computation of bit score it requires the parameter K and lambdam. Most of the document only mention it as a statistical parameter but didn't talk about how to compute it, do the information provided from the pairwise2 module enough to compute K and lambda or I should use another algorithm to find the bit score? I do also find some document mentioned that K and lambda can be derived from my scoring system, does it means my score matrix?