Nucleotide mutations for Usher tree

[jeromekelleher]

I think we're using the Taxonium output for the current tree translation which is nice and easy for the topology.

We should be able to get the actual nucleotide mutations out by using the protobuf version instead to extract the nucleotide mutations.

There's a matutils command matUtils summary --translate which should list all mutations per node in nucleotide form.

https://usher-wiki.readthedocs.io/en/latest/matUtils.html#summary

[jeromekelleher]

I think we need to do this to make any meaningful comparisons of the trees.

[jeromekelleher]

Has anyone got usher installed on their system to try this out (or a working conda installation)? I can't be bothered setting up conda here, and it seems like the only straightforward way to install.