trimming phylogenetic tree

[mario1988]

Hello,

I have a question regarding trimming a phylogenetic tree. In particular, I would like to delete a list of terminal nodes from the tree, but still preserve the internal nodes of their last common ancestor. For example, if I have a tree like this:

---------1
|
---3
| |
| ---------2
--|
|
| ---------5
| |
---4
|
---------6

(sorry that the tree is poorly drawn, but in this tree, 3 is the LCA of 1 and 2, and 4 is the LCA of 5 and 6)

I would like to trim both 1 and 2, but to preserve 3, in which case the tree will to become:

----3
|
|
--|
|
| ---------5
| |
---4
|
---------6

I know there is a function in bio:treeio called remove_Nodes, however it would remove both terminal nodes and internal nodes (in this case, all the nodes 1, 2 and 3 will be removed) from the tree, which is not what I want.

I wonder if anyone knows how to do this. Thanks!

Zhang

[mbblack]

The only software you need to do this is a simple text editor. Just save the tree as a Newick tree format file. Newick files are text files, so then just edit the series of nested parenthesis that describes the dendogram structure, save it and open it in any one of the many free tree drawing tools.

If you've never heard of the Newick file format then just take a look at:

http://wiki.christophchamp.com/index.php/Newick_phylogenetic_tree_format

P.S. if branch lengths are important in your analyses, you should re-optimize them after editing the treefile as removing those two terminal nodes will alter relative branch lengths.

[mario1988]

mbblack, thanks for your reply! I can easily manually edit the newick file for one tree. However I have 100 trees like this, so individually editing each one instead of writing a script might be hard..

thanks anyway!