Hi, I am Yunjun Zhang from Peking University, China. I am using nextstrain to analyze the sequence data of SARS-CoV-2. I have two questions about the “clock” view of the tree. 1) I am wondering if this clock view of tree is the same as the root-to-tip plot of the tree in the software of Tempest (a package of BEAST). 2) How to calculate the “rate estimate” displayed in the clock view. It seems that the solid black line is not the ordinary least squares regression line of all the tips. I have been searching for a while for the documents about the algorithm/method used in the “clock” view, but I havn’t got any. I’ll be very appreciated if anyone can explain this to me.
Best regards