[Bioperl-l] TreeIO, how (does) it work?
flope004 at hotmail.com
Mon Feb 12 13:07:12 EST 2007
thanks for your reply!
I am using Bioperl 1.4.
>Node 6 is to hold the root or a fake root with a trifurcation for
>unrooted trees. Did you actually call the reroot method to set the
>root to node 5?
Yes, I tried the following with the same result:
$tree->reroot($tree->find_node(-internal_id => '5'));
$tree->set_root_node($tree->find_node(-internal_id => '5'));
Even if I use a rooted tree:
I get the node #6. So, is it always present? Am I not representing properly
a rooted tree in newick format?
>The distance method is just summing branch lengths on the path
>between two nodes. Is that what are you trying to do?
>The error message you report doesn't make sense as
>"Must provide a valid array reference for -nodes"
>is only printed when you call is_monophyletic or is_paraphyletic as
>far as I can tell.
I do not know yet what I was doing incorrectly but now It works. Yes, I was
using the distance method to know where the node 6 was located. For the
unrooted tree, node 6 was node 5 (an internal node) and for the rooted tree
node 6 was 0.1 from the mouse leaf and the internal node (root).
The error message: "Must provide a valid array reference for -nodes" is
shown if I indicate a node which is not present in the tree.
>You are trying to calculate the likelihood of a tree or are you
>trying to generate a ML tree from an alignment?
I am trying to calculate the likelihood of a tree, as a practice. Probably
there are other bioperl modules, besides AlignIO and TreeIO, which can help
me in the process and I do not know them.
Again, thank you for your time!
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