As we have seen, there are two different log-odds scoring matrices available. When performing pairwise sequence alignments, you must specify the exact matrix to use - this depends on the suspected degree of identity between the query and its matches.
Let's do a quick summary of these two matrices and see how they differ.
PAM (Accepted Point Mutations) matrices are:
Some limitations of PAM matrices include the somewhat inaccuracy of the assumption model and each position being context dependent.
Limitations are that you are limited to a subset of conserved domains.
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