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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: