Eric Ma

@mtholder: thanks for the suggestion! I'm going to try experimenting with increased recursion limits to see what works for our use case.

@mtholder: increasing the recursion limit worked! Thank you for the tip. Meanwhile, I will check in with my colleagues to see if I can share the trees with you -...

Hi @jeetsukumaran, thanks for helping out! Our trees were on the order of ~50,000 taxa. I was doing patristic distance computations on them, figuring out which were the phylogenetically closest...

We wrote custom calculations, because it was taking a long time to compute all pairwise patristic distances (~more than a few hours, and I never let the computation finish).

@lucajovine thanks for confirming that the extra CPU cores help! I’m wondering if we might be able to keep the issue open to get a second opinion from the AF2...

Colab's going to be a bit tricky. They don't support the installation methods that we are used to, as it presumes a fixed, ephemeral VM that you install packages into,...

@hugobowne yep, that's right! > can do this manually by making sure all cells execute in order; can you remind me of how to automate this step? Use `nbconvert` to...

@hugobowne I updated your comment with further details, so we both have a reference in this issue right at the top of the thread.

@akgopan the you would want to use the posterior trace object, which contain draws from the posterior. I have done this by using draws from the posterior in agent-based simulations...

I was struggling for the right words, thanks @justinbois!