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Slack / Private Message Drop, p.300 [SLACK_000514] · slack_pm:msg:03137

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I think it's safe to say that we're definitely missing some early emergence stuff here

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-12-06 11:14 Andrew Rambaut open

Given it is synonymous and the pangolin has loads of other mutations in that area it must be coincidence.
2020-12-06 11:15 Kristian G. Andersen open

Oh, but hang on - RmYN02 has 'C' in this position too - so pangos and RmYN02
2020-12-06 11:15 Andrew Rambaut open

But spooky none the less
2020-12-06 11:15 Kristian G. Andersen open

Yeah, probably - but, yes, spooky.
2020-12-06 11:15 Kristian G. Andersen

I think it's safe to say that we're definitely missing some early emergence stuff here
2020-12-06 11:16 Kristian G. Andersen open

... which is very interesting and worth a closer look. Would explain why we can't really root properly as well (Ihaven't checked recently, but back in the spring, BEAST insisted on a midpoint root when you took away the dates).
2020-12-06 11:16 Andrew Rambaut open

Will do some experiments on BEAST dating with enforced WA1 outgrouping
2020-12-06 11:17 Kristian G. Andersen open

Okay, cool - I'll have a chat with Karthik too - we haven't been able to get good estimates of the root TMRCA recently, but that may very well be on us.
2020-12-06 11:18 Kristian G. Andersen open

I'm heading out for an hour, but once I'm back lemme just clean up these alignments a little and share - just so wehave them archived here. :beer: