[Biojava-l] A question about NexusFile and NewickTreeString

[huijieqiao at gmail.com]

Hi Tiago,

I used the tree "(A,B,(C,D)E)F;" comes from wikipedia and get the same error

http://en.wikipedia.org/wiki/Newick_format  "the 3rd one"

(,,(,));                               *no nodes are named*
(A,B,(C,D));                           *leaf nodes are named*
(A,B,(C,D)E)F;                         *all nodes are named*
(:0.1,:0.2,(:0.3,:0.4):0.5);           *all but root node have a
distance to parent*

(:0.1,:0.2,(:0.3,:0.4):0.5):0.0;       *all have a distance to parent*
(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);       *distances and leaf names* *(popular)*
(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;     *distances and all names*

((B:0.2,(C:0.3,D:0.4)E:0.5)F:0.1)A;    *a tree rooted on a leaf node* *(rare)*



2009/12/15 Tiago Antão <tiagoantao at gmail.com>

> On Tue, Dec 15, 2009 at 2:19 AM, huijieqiao at gmail.com
> <huijieqiao at gmail.com> wrote:
> > Hi all,
> >
> > I have a NexusFile like this:
> >
> > #NEXUS
> >
> > Begin TREES;
> >    tree test1 = (1,2);
> >    tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0)
> > Ancestor1:5.0,D:11.0);
> > End;
> > How can I deal with this ?
>
> There is a comma missing after the ) closing E:4.0) ie,
> >    tree test2 = (B:6.0,(A:5.0,C:3.0,E:4.0), <-- NOTE COMMA
> > Ancestor1:5.0,D:11.0);
>
>
> --
> “Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci
>