[Biojava-l] Rooted trees in nexus files

[Hilmar Lapp]

The most common ways to root a tree is by mid-point rooting, or using  
an outgroup. The latter I suppose is equivalent as the user specifying  
a node as the root.

	-hilmar

On Nov 3, 2009, at 4:56 AM, Richard Holland wrote:

>
> On 2 Nov 2009, at 23:11, Tiago Antão wrote:
>
>> 2009/11/2 Richard Holland <holland at eaglegenomics.com>:
>>> In the meantime, the JGraph library which is used for displaying  
>>> JGraphT
>>> graphs in a visual form does include root-finding methods, so  
>>> maybe you
>>> could investigate there to see if any of the existing functions  
>>> might help?
>>
>> Did that. None can help as the graph is not directed (it would be
>> trivial with a directed graph ,of course).
>> In the current form, the nexus parser is of limited use for tree  
>> information:
>> 1. For rooted trees it has a bug has it doesn't say what is the root
>
> The Newick strings used in the Nexus format are themselves  
> undirected graphs. They don't specify which node is the root, which  
> means it must be determined by computation after parsing the string.  
> I'm unsure of the algorithm to use to do this. If there are people  
> on this list who know the algorithm and have time to code it up,  
> volunteers would be welcome.
>
>> 2. For unrooted trees, sometimes the "root" (what the user perceives
>> as root) is interesting information.
>
> What the user perceives as root in an unrooted tree could be  
> different for every user, so it would be hard to provide a standard  
> function to read their mind! However if everyone can come up with a  
> commonly agreed way of determining the most likely root  
> computationally, it would be interesting to add this as a feature,  
> with the caveat that it is only a best-effort approximation as the  
> original tree is unrooted.
>
> cheers,
> Richard
>
> --
> 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/
>
>
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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