[Bioperl-l] Find distances between LCA's and the other nodes from a tree

Ross KK Leung ross at cuhk.edu.hk
Mon Oct 3 13:41:27 EDT 2011


Thanks Tom. This is the 2nd time you help me. Suppose I change the structure
to:

 

((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G;
 
I have identified two problems.
 
1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a
warning will prompt and the value shown is wrong). 
2) Nodes F, E and G are annotated by me, but in fact the newick tree
generated does not contain any ID. So that means I have to manually
supplement ID's for such intermediate nodes before further processing (this
is indeed dealing with "recursive descent parsing" myself...)? 


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