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Post date: Jul 06, 2020 11:2:14 PM

Hi Rozenn,

Nice job today.

A few things to follow-up.

1. Lets start with BEAST (unless you find something else you prefer).

Here is the original paper about the software:

There is a bunch since then if you want to dig in more (maybe look at

some recent examples and their website).

2. ANGSD is what I thought of today for estimating the effective number

of sites. You can read about it in general here,

And here is a help page that includes effective number of sites.

3. I also really like the diversification rate through time/lineage

thinking.

Here is a simple example from a colleague of mine:

Here is another classic example:

And this is a recent(ish) method. Maybe start there and see what you can

find.

4. I am around until the middle of next week then gone for a few weeks

in the field (still e-mail contact, but less). It might be good to take

a few days to read and think and then to meet early next week?

Cheers,

Zach

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