Unable to view node.label / posterior probability values in R

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Vijay Ramesh

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Feb 15, 2017, 3:39:52 PM2/15/17
to ggtree
Hi All.

I read in a tree that was the consensus tree from MrBayes in .nwk format. 
The problem is when I load it into the global environment, I clearly see only the edge, Nnode, tip.label and edge.length.

Any idea on how to make my post. prob values appear? If I view the same tree in FigTree, I can see the prob values when I select "prob" under Node Labels column.

Suggestions?

vijay

Yu, Guangchuang

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Feb 15, 2017, 9:12:13 PM2/15/17
to Vijay Ramesh, ggtree
Is the tree you read in FigTree also the nwk one you parsed into R?



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Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
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Vijay Ramesh

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Feb 16, 2017, 9:22:51 AM2/16/17
to Yu, Guangchuang, ggtree
The tree I read in Figtree was a .tre file. 

Here's the thing. I had to first open the .tre file in Figtree to convert it to a .nwk format to read it in ggtree. 


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Vijay Ramesh,
Cary Institute of Ecosystem Studies,
Millbrook, New York 12545



Yu, Guangchuang

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Feb 16, 2017, 9:58:05 PM2/16/17
to Vijay Ramesh, ggtree

So you couldn’t expect it to work since you are using different tree files.

Actually, when you export the tree to nwk format, you lost all the evolution inferences.

MrBayes output is supported in devel branch of ggtree, but in current release version.

If you are using ggtree 1.6.X branch, you can open your tree in Figtree and save it in tre file (actually Nexus format). Figtree will convert it to BEAST NEXUS format, and then you can parse the tree into R using read.beast.

If you are using ggtree 1.7.X branch, MrBayes is supported. You can also use read.beast, which was extended to support MrBayes.

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