Question: Visualize Tree In Phylobayes
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gravatar for ce13210
3.9 years ago by
ce132100
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 • 1.1k views
ADD COMMENTlink modified 25 days ago by Biostar ♦♦ 20 • written 3.9 years ago by ce132100

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

ADD REPLYlink written 3.9 years ago by youngcsong100
0
gravatar for obrien.jeffreym
10 months 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:

    setwd("~/Desktop/tree_here/")

  2. load Ape:

    library(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 10 months ago • written 10 months ago by obrien.jeffreym0
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