How to fixed year scale in FigTree

[Oshin Ley Garcia]

Hi everyone,

Thank you again for all the advice that has helped me run my models smoothly.

I am currently comparing PCV3 sequences from wild and domestic pigs. The viruses were isolated between 2018 and 2024, and in BEAST I used tip dates as years and included host as a trait. All parameters look good and I have approximately 70 sequences (see picture attached).

My issue appears when I visualize the MCC tree in FigTree after running TreeAnnotator. No matter what I try, I cannot get the x‑axis to display the correct calendar years. I have already tried enabling both “Scale Axis” and “Time scale,” but the scale still does not show the expected years. I also attempted to plot the tree in R, but I end up with two different results. 

If anyone has experience fixing this issue or can point me to the correct settings to properly display calendar years in FigTree, I would really appreciate your guidance.

Find picture enclose color represent domestic and wild pigs 

[Sikandar Azam]

Hi oshin,

To add a time axis in FigTree, open the Time Scale panel from the sidebar menu. Select Scale by factor, and then set the Offset value to the most recent sampling date in your dataset. In the figure shown, the Offset is currently set to 0, which will not produce the correct calendar time scale. Replace 0 with the most recent sampling date to properly calibrate the time axis.  

I hope this tutorial helps: https://beast.community/workshop_figtree

Best,  

Sikandar

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[Oshin Ley Garcia]

Hi thanks for your time. That actually works and fixed the issue.