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

[Albert Vilella]

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:

(Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5;

Instead of what has to be...

((Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5);

...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?

E.g.:

(Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239):0.000000);

Thanks in advance,

Bests,

    Albert.