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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?

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  • $\begingroup$ 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. $\endgroup$
    – NatWH
    Mar 3 at 10:53
  • $\begingroup$ See page 49 of the RAxML v8.2.X manual $\endgroup$
    – NatWH
    Mar 3 at 10:59
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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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