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 <[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/
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
