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Bayesian skyline plot issues in BEAST.v2.4.7 #9

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DuPanxin opened this issue Jul 7, 2022 · 0 comments
Open

Bayesian skyline plot issues in BEAST.v2.4.7 #9

DuPanxin opened this issue Jul 7, 2022 · 0 comments

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@DuPanxin
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DuPanxin commented Jul 7, 2022

Dear Professor,

Very sorry to bother you with small issues! But I really encounter some issues about using Beast.

I am a beginner at beast and I am doing coalescent Bayesian skyline plot analysis for a populaton about 300 human mtDNA sequences using BEAST.v2.4.7. I selected the coalescent Bayesian skyline model and bPopSizes=5 in BEAUti.
Then, I selected the Stepwise (Constant) in Tracer.
After visualizing in Tracer v1.7.2, I found two issues:
First,the two HPD lines are merged with median line within 5000 years.
Second, the time in x-axis for these lineages is usually 5-70,000 years before present in previous mtDNA studies, but in my plot is just 25,000 years. I wonder if it is beacuse I did not set the calibration node ? I attcahed the figures of these issues(https://groups.google.com/g/beast-users/c/AeS_xLgA8zI).

What are the reasons and how could I solve these issues? It would be very appreciated if you can help me.

Looking for your reply.

Sincerely,
Panxin Du

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