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Branch-models are currently not implemented in godon. In the PAML manual Ziheng Yang writes: This model is very parameter-rich and its use is discouraged. This was one of the reasons I did not implement it. Disclaimer: I am the author of godon.


You need to iterate over the sequence 3 characters at a time and you need to stop when you hit the stop codon (or before for an invalid codon, e.g. of length 2). Here is a memory efficient implementation using iterators (requires python >= 3.8): from itertools import islice def protfromRNA(Seq): it = iter(Seq) lst = [] while codon := "&...

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