<ol>
<li>if you read it into FigTree then in the export in Nexus and perform a &quot;save all trees&quot;  it should then read into <code>read.beast()</code>.</li>
<li>Use the beast file output before you performed tree annotator operation.</li>
</ol>
<p>1 or 2. should be read directly into <code>read.beast()</code>.
I would try option 2 first.</p>

CC BY-SA 4.0
2023-10-12T12:11:18.287Z
2023-10-12T13:23:07.753Z
2023-10-12T13:23:07.753Z
M__
<p>I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using <strong>BEAST1</strong> and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to import it into <strong>R</strong> for editing, but I run into an error when using the <code>read.beast()</code> function from the <strong>treeio</strong> package:</p>
<pre><code>MCC_tree &lt;- read.beast(&quot;/home/MyPC/Downloads/MCC_beast.tre&quot;)
Error in FUN(X[[i]], ...) : 
  numbers of left and right parentheses in Newick string not equal
</code></pre>
<p>Interestingly, when I attempt to visualize the tree using figtree, it works fine. Likewise, importing into R using <code>read.nexus()</code> works without issues. However, I want to use <code>read.beast()</code> specifically because I need to annotate the &quot;posterior&quot;, which I can't do when I import it using <code>read.nexus()</code>.</p>
<p>Has anyone encountered a similar issue or have any suggestions on how to resolve this?</p>
<p>Thank you in advance!</p>

<r><phylogenetics><phylogeny><bioconductor><ggtree>
Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()
# Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()

(Asked by: username_0 on 2023-10-12)

I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to import it into R for editing, but I run into an error when using the read.beast() function from the treeio package:
MCC_tree <- read.beast("/home/MyPC/Downloads/MCC_beast.tre")
Error in FUN(X[[i]], ...) : 
  numbers of left and right parentheses in Newick string not equal

Interestingly, when I attempt to visualize the tree using figtree, it works fine. Likewise, importing into R using read.nexus() works without issues. However, I want to use read.beast() specifically because I need to annotate the "posterior", which I can't do when I import it using read.nexus().
Has anyone encountered a similar issue or have any suggestions on how to resolve this?
Thank you in advance!

**Tags:** r, phylogenetics, phylogeny, bioconductor, ggtree

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## 1 answers

### Answer by username_1 on 2023-10-12. Score: 0

1. if you read it into FigTree then in the export in Nexus and perform a "save all trees" it should then read into `read.beast()`.
2. Use the beast file output before you performed tree annotator operation.

1 or 2. should be read directly into `read.beast()`.
I would try option 2 first.


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