Katherine Eaton

> This precludes a straightforward implementation of sc2rf in our pipeline. The recombinants with very few alleles contributed by a donor (ex. XP, XT) are extremely difficult to detect systematically...

I just wanted to say thank you for this super detailed discussion! :) I'm still thinking and testing it out, but this has helped a lot!

Would this be using the tree from the [nextstrain monkeypox build](https://nextstrain.org/monkeypox)? Or is there another pre-built public phylogeny?

This is amazing thank you! I'll be cautious with usage and interpretation since it's in early development