Hi, I try to use BEAST software for estimating divergence times for some of fungal species/populations. I use sequence data of five coding regions and do not use any fossil calibaration. One of the biggest trouble for me, I can not put or see or interpret time scale when I illustrate output of BEAST on Figtree. Does anybody have any idea or suggestion? Or any other user friendly software suggestion for that? Thanks....
Hi,
If you have serially sampled sequences you can use the sample dates (dated tips) to calibrate the molecular clock. Check out this page, there are nice tutorials available. Also for annotating the maximum clade credibility (MCC) tree to time scale your phylogeny in Figtree
http://beast.bio.ed.ac.uk/
Have fun!
W.
Thanks Cornelis, but my samples are not serialy sampled. And thanks Alex, so you mean to use substitution rate?
Thanks Artur! Do you know also how to show time scale under the tree based on substition rate for illustration? I was not able to see this opton in Figtree. Thanks...
The fig tree has an option SCALE AXIS. tick that and you will get your time scale.
Go to "time scale" - set up - "Offset by" your latest year on your tree (2017 for instance); the "scale factor" to 0.1 because we usually do not work more than 50 years range. then Go to "scale axis" and tick the "Reverse axis" and untick and tick again the "automatic scale". You should be able to see your tree aligned with the year scale bar. you can increase the font to 15-20. (note - I usually remove the scale bar when I do this setting)
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