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

[Albert Vilella]

I respond to myself:

There is a bit of commented code in newick.pm +237:

       if($data[-1] !~ /\)$/ ) {
	   $data[0] = "(".$data[0];
	   $data[-1] .= ")";
       }

That if it is commented out, will add the latest pair of parenthesis.

Does anybody know why this is commented?

Any problem if I sync this in CVS?

    Albert.

El dl 14 de 11 del 2005 a les 11:16 +0100, en/na Albert Vilella va
escriure:
> 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.
> 
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