On 2 Nov 2009, at 23:11, Tiago Antão wrote:
2009/11/2 Richard Holland <[email protected]>:
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: [email protected]
http://www.eaglegenomics.com/
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