visualization of IQTree output

[tarakaramji M]

Dear Admin,

I am trying to visualize and convert my phylogenetic tree to PDF format displaying all the support values using ete3.

IQTree phylogenetic trees are different from Raxml tree as they have three support values like 100/1/100

I installed ete3 and used the following command

ete3 view -t treeedited.treefile

and the error is

ete3.parser.newick.NewickError: Unexpected newick format '100/1/100:0.154567' 

You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

IQTree webserver somehow uses ete3 to visualize the tree.

Any help will be highly appreciated.

Thanks

Ramji

[Jaime Huerta Cepas]

Hi Ramji, 

this is a very particular newick format. I see two solutions: 

1. parse the newick string with a regular expression that chooses which of the three values (100/1/100) is the one considered as branch support and therefore convert 100/1/100: into 1: 

2. Load the newick using format=1, which assumes that 100/1/100 is the name of the branch. You can then process the tree and iterate over nodes parsing the name string and loading support values manually. In example: 

tree = Tree("newick", format=1)

for node in tree: 

  if not node.is_leaf():

   node.support = float(node.name.split("/")[1])

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