calculating pairwise divergence times for large dataset

[Kartinaa]

Dear OpenTree Team,

I hope this message finds you well. I am writing to ask whether there is a way to calculate pairwise divergence times for a large dataset (approximately 32,000 species) using OpenTree resources. I would like to incorporate these divergence times into my research and want to ensure I am following the most efficient and appropriate approach.

Any guidance on how to perform this computation, whether through existing tools, downloadable data, or api, would be greatly appreciated!

Thank you very much for your time and assistance. I hope you have a great day!

[snacktavish]

Hi! Sure - that is definitely possible!

There are a few approaches. We used one here: https://www.pnas.org/doi/10.1073/pnas.2409658122 and a related one in this paper: https://www.biorxiv.org/content/10.1101/2025.08.12.669825v1

They both rely on dates from Chronosynth https://github.com/OpenTreeOfLife/chronosynth/wiki/Chronosynth-methods-overview which is not published, or very well documented yet, but it is functional!
There is a python tutorial here https://github.com/McTavishLab/jupyter_OpenTree_tutorials/blob/master/notebooks/DEMO_DatedTree.ipynb of how you could get dates for a set of names.

Alternately, you could use DateLife - https://academic.oup.com/sysbio/article/73/2/470/7632550, but I think it would struggle for that many taxa! (@LunaSare what do you think?)

I would also note that chances are OpenTree does not have any data on divergence times for many of your pairs (depending on what taxa they are), and therefor some imputation will be necessary.

@jdduke24 is working on interpolation of dates across the whole tree, but I'm not sure if he is ready to share his results yet.

I'm happy to follow up with other questions if any of these approaches seem like they could be a good fit!