What is the error of this Nexus file? I cannot open it in Figtree
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12 weeks ago
fhsantanna ▴ 520

I want to open the following nexus file in Figtree: https://we.tl/t-AYsbwPhOr1

However, I am getting the following error:

"Error reading tree file: Number format error: For input string: 0.006486150556156645)NODE_0004110

In R, I got the following error:

nexus <- treeio::read.beast(file = "example.nexus")

Error in FUN(X[[i]], ...): numbers of left and right parentheses in Newick string not equal

Traceback:

  1. treeio::read.beast(file = "example.nexus")
  2. read.stats_beast(file)
  3. read.stats_beast_internal(beast, trees)
  4. read.tree(text = tree)
  5. lapply(STRING, .treeBuild)
  6. FUN(X[[i]], ...)

I was not able to identify the problem of the nexus file generated by auspice. Could you give me a clue? I need the data between the brackets, because I have to color the tree according to the "localidade" variable.

figtree ggtree R phylogenetics • 249 views
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The R error tells you the reason it fails: There seems to be an unmatched "(" or ")" in the Newick string. Double-check where you got the tree from, please.

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Yes. The tree was generated in Auspice (auspice.us). At least the number of "(" and ")" are the same. The main problem is that I need to work with a tree containing 4000 leaves, it would be difficult to check the parentheses pairs.

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