[Bioperl-l] Bio::Tree newick and internal nodes

Albert Vilella avilella at ub.edu
Mon Nov 14 05:16:30 EST 2005

Hi all,

I'm having a trouble with the newick module when trying to print out
the tree coming from a mlc codeml result file. There is some
combination of internal node arrangements that gives this tree:


Instead of what has to be...


...to play well with some programs (PAML's evolver in this case).

Any hint if this is/should_be ok?

Also, is there a way to print out a newick tree in which only the leaf
nodes have the ids printed?



Thanks in advance,



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