Question: Visualize Tree In Phylobayes
gravatar for ce13210
6.2 years ago by
ce132100 wrote:

Hi I am using Phylobayes and I need to visualize the .con.tree file after using the READBP command How canI visualize the tree in a phylogenetic manner?

visualization tree • 1.8k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 6.2 years ago by ce132100

To which format does Phylobayes print out the trees? Is it newick format?

ADD REPLYlink written 6.2 years ago by youngcsong100
gravatar for obrien.jeffreym
3.2 years ago by
obrien.jeffreym0 wrote:

I was having the same problem. Here is how I solved it:

  1. Set the proper working directory where your tree is located:


  2. load Ape:


  3. Read the tree into R using Ape:

    tree <- read.tree("dayhoff_bpcomp.con.tre")

  4. Write the tree to an output file using Ape:

    write.tree(tree, file = "tree.newick.tre")

I'm not sure why this works, as I cannot see any meaningful difference between the original tree and tree.newick.tre, they even have the same number of characters! However, once I went through these steps, figtree had no problem opening the tree.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by obrien.jeffreym0
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