Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-04T05:41:40.677Z
Answers.LastActivityDate: 2021-03-04T05:41:40.677Z
Answers.UserDisplayName: YP CHEN
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-03T10:53:00.500Z
Comments.Text: 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.
Comments.UserDisplayName: NatWH
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-03-03T10:59:23.733Z
Comments.Text: See page 49 of the [RAxML v8.2.X manual](https://cme.h-its.org/exelixis/resource/download/NewManual.pdf)
Comments.UserDisplayName: NatWH
Tags: <r><phylogeny><ggtree>
Title: How to import a phylogenetic tree (in nexus format) with node support values in R
ThreadText: # 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)  
  
  ---
  
  ## 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]
  
  
  ---
  
  