Question: ggtree: time-scaled tree s
0
gravatar for aelgorriaga
2.2 years ago by
aelgorriaga0 wrote:

Hi everyone!

I'm having problems trying to use the time-calibrated tree on ggtree, because I basically don't understand how to do it.

I have some 40 taxa, mostly fossils, of which I know a minimum and a maximum age.

I've used timePaleoPhy of the paleotree package in the past, with that I entered the table contaning the name of the taxa, minimum age, and maximum age, and separately a phylogenetic tree. Then proceeded to calibrate that tree with the ages from the table. 

Does ggtree has a similar function? it is involving mrsd? could someone give me an example? All the examples that I have seen so far are involving DNA and sampling dates, and that's not helping me at the moment. 

Sorry for the (probably) super basic question but my R coding skills are very limited.

ADD COMMENTlink modified 2.2 years ago by Guangchuang Yu1.1k • written 2.2 years ago by aelgorriaga0
Answer: ggtree: time-scaled tree s
0
gravatar for Guangchuang Yu
2.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
Then proceeded to calibrate that tree with the ages from the table. Do you mean you are using the paleotree to infer time to MRCA? I don’t know the paleotree package, but if it can be used to process your data and give you the time-scaled tree, then you can use it and using ggtree to visualize the output tree. Basically, ggtree is designed for visualization and annotation of phylogenetic tree and without features to infer TMRCA. We rely on other software (e.g. BEAST) to do the inference. ​
ADD COMMENTlink written 2.2 years ago by Guangchuang Yu1.1k
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