[Biojava-l] Rooted trees in nexus files

[Richard Holland]

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/