Can ancestral_reconstruction.py be used for amino acid sequences ?

[ghost]

@rneher Can ancestral_reconstruction.py be used for amino acid sequences ?

[rneher]

yes, when used as a python library. You can use arbitrary alphabets and GTR matrices. I still need to expose this to the command line.

[ghost]

I used amino acid sequences for mugration model, it showed nucleotide mutation, for example, A334G, not amino acid mutation?

[rneher]

thanks for point this out. we had never really used the amino acid functionality and it was somewhat hidden and buggy, I cleaned this up a bit. If you update treetime to current master, amino acid reconstructions should work as described here: https://github.com/neherlab/treetime_examples/blob/master/ancestral.md#amino-acid-sequences

[ghost]

@rneher thanks.