Thread Subject: Renaming leaves in tree obj in Bioinformatics toolbox

Greetings,

This is a question on behalf of a friend of mine who is using the bioinformatics toolbox. Since I don't use it, I can't answer it, but I
thought I'd post it here:

"I have a 'phylogenetic tree' object in matlab, and I want to leave all of it alone except the LeafNames, where I want to swap one vector
for another one of the same length, but with different values as the entries. How the heck do I do that?"

My understanding is that the leaf names on an existing tree can't be changed. But the first thing that came to mind is to re-create the
tree with the same info but with the desired names.

I suggested this but he said that he had loaded the tree from a newick formatted file using phytreetool. He tried "to save the tree into
newick, remove [the names], and bring the tree back - it reorganized the branches so that all the ordering of tree related data and such I
had done was moot."

Any pointers?
-Mark

You should be able to do something like this:

tr = phytreeread('your newick file')
p = get(tr,'pointers')
d = get(tr,'distances')
names = {'name 1','name 2','name 3','name 4'};
% you should have as many leaf names as in
% the original tree
newtr = phytree(p,d,names);
view(newtr)

I hope this helps, let me know if you have any other question

Lucio Cetto
The MathWorks, Inc.

 Cueball wrote:
>
>
> Greetings,
>
> This is a question on behalf of a friend of mine who is using the
> bioinformatics toolbox. Since I don't use it, I can't answer it,
> but I
> thought I'd post it here:
>
> "I have a 'phylogenetic tree' object in matlab, and I want to leave
> all of it alone except the LeafNames, where I want to swap one
> vector
> for another one of the same length, but with different values as
> the entries. How the heck do I do that?"
>
> My understanding is that the leaf names on an existing tree can't
> be changed. But the first thing that came to mind is to re-create
> the
> tree with the same info but with the desired names.
>
> I suggested this but he said that he had loaded the tree from a
> newick formatted file using phytreetool. He tried "to save the tree
> into
> newick, remove [the names], and bring the tree back - it
> reorganized the branches so that all the ordering of tree related
> data and such I
> had done was moot."
>
> Any pointers?
> -Mark
>