[Biojava-l] Rooted trees in nexus files

[Richard Holland]

Agreed that there is a bug. Now all we need is someone to go in and  
fix it! :)

cheers,
Richard

On 3 Nov 2009, at 18:16, Tiago Antão wrote:

> 2009/11/3 Thasso Griebel <thasso.griebel at uni-jena.de>:
>> There is a way to uniquely  get a root from a newick string.  
>> Usually a
>> rooted newick is surrounded with brackets, which indicates the root  
>> as the
>> highest node in the tree. For example:
>>
>> (A, (B,C))
>>
>
> Agree, it is quite easy to get the root of the tree from the newick
> representation. But it should be done on parsing and returned in some
> way by the parsing system. If the user has to do it again, it means
> that the user has to parse it again just to know the root node.
>
>> I would also suggest to generally parse trees as rooted trees  
>> (maybe jsut
>> for th initial internal model). Creating an unrooted tree from a  
>> rooted  one
>> is easy, remove the root and forget about directions. The other way  
>> might be
>> hard and ambiguous.
>
> 100% agree.
> The newick _representation_ always has a root by virtue of the way it
> is done. If that root has meaning or not depends. Doing as you suggest
> seems the most reasonable idea.
> I would add that even if it is an unrooted tree, the topology might be
> of interest. In my case I am doing a comparative visualizer and it
> might be nice for the user to be able to visualize the topology as
> specified. It has no biological meaning, but in practice, for many
> users, it helps.
> I note that PhyloXML (even by virtue of being a XML format) always
> represents the phylogenies as trees (not weigthed DAGs). There an
> attribute rooted which can be true or false.
>
> But, anyway. Even assuming a very conservative view on this, the
> current parser, for rooted trees, does not allow to determine where is
> the root. I think that there would be a consensus that that is a bug?
>
> Tiago

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/