How to compare any two pair of sequences in A fasta file

Question

[eadonyo]

Hello, I have a fasta a file consisting of multiple samples of sequences that are already aligned. Please help me with a python code that compares any two sequences within the file for evidence of Nonsynonymous: Synonymous substitutions (dN/dS).

Answer 1

[Joe]

Don't write your own code unless you really need to. Use something like PAML which is already designed for this.

https://www.ncbi.nlm.nih.gov/pubmed/25388108