My nexus file can be displayed in R, but can not in Figtree

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13 months ago

wukunouc • 0

I run MCMC tree in beast2, and I got a tree file (listed in NEXUS format). I can display it in R or iTOL, but I can't disply in Figtree, shall anybody help me to figure out this issue? Here is my NEXUS file: https://www.notion.so/My-nexus-file-03d153a6d19c4bdbbce83467b9ab7691

My tree in R: My tree displayed in figtree: tree in Figuretree

beast figtree • 562 views

ADD COMMENT • link 13 months ago by wukunouc • 0

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Tough to tell as these images have low resolution and are difficult to read. If FigTree is not throwing an error of some kind, it means that the tree is read in correctly, but the display is off.

I think you need to move your sliders from the far left positions to the right and you will start seeing things. As of right now, everything you have is set to size 0, and "Zoom" especially needs to be more to the right.

ADD REPLY • link 13 months ago by Mensur Dlakic ★ 27k

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Thanks for your kind help! I adjusted "Zoom", but it only increased spacing between sample ID. enter image description here if I use transform branches parameter, the cladogram can be showed: So I wonder if there is something wrong with my NEXUS file,e.g, negative branch lengths or incorrect weight?

ADD REPLY • link 13 months ago by wukunouc • 0

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