Hi. Newbie here.
I’m wondering why does the tree generated using ncov sequences has dates earlier than December 2019 when it should have been the earliest date, since Wuhan-Hu-1’s collection date is 26 Dec 2019. Any idea? Thanks a lot.
The time information of internal nodes (the one without circles) comes from running TreeTime.
TreeTime uses a statistical model to estimate when various common ancestors may have evolved. But as with any statistical model, if some of the assumptions are violated the results can be wrong.
TreeTime doesn’t know what you know: that it’s unlikely that the spillover happened after Nov 2019.
The tree may also not be perfect due to tree building errors and sequencing artefacts.
I hope this helps
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This clarified everything. Thanks a lot.