<p>I recommend you this tutorial about ggtree. You will find the solution.
[https://guangchuangyu.github.io/ggtree-book/short-introduction-to-r.html][ggtree]</p>

CC BY-SA 4.0
2021-03-04T05:41:40.677Z
2021-03-04T05:41:40.677Z
YP CHEN
<p>I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when I import the tree file in R with the read.nexus function in ape, the node values do not appear in $node.labels. Can someone recommend another option in R?</p>

CC BY-SA 4.0
2021-03-03T10:53:00.500Z
RAxML, or raxml-ng? The former has both a bipartitionsBranchLabels file with a weird support formatting in the newick, where the support values are wrapped in square brackets ([ ]) and a bipartitions file, where they are normally formatted.
NatWH
CC BY-SA 4.0
2021-03-03T10:59:23.733Z
See page 49 of the [RAxML v8.2.X manual](https://cme.h-its.org/exelixis/resource/download/NewManual.pdf)
NatWH
<r><phylogeny><ggtree>
How to import a phylogenetic tree (in nexus format) with node support values in R
# How to import a phylogenetic tree (in nexus format) with node support values in R

(Asked by: username_0 on 2021-03-03)

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when I import the tree file in R with the read.nexus function in ape, the node values do not appear in $node.labels. Can someone recommend another option in R?

**Tags:** r, phylogeny, ggtree
> **Comments:**
> **username_1**: RAxML, or raxml-ng? The former has both a bipartitionsBranchLabels file with a weird support formatting in the newick, where the support values are wrapped in square brackets ([ ]) and a bipartitions file, where they are normally formatted.  
> **username_1**: See page 49 of the [RAxML v8.2.X manual](https://cme.h-its.org/exelixis/resource/download/NewManual.pdf)  

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## 1 answers

### Answer by username_2 on 2021-03-04. Score: 2

I recommend you this tutorial about ggtree. You will find the solution.
[https://guangchuangyu.github.io/ggtree-book/short-introduction-to-r.html][ggtree]


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