[Biopython-dev] [Bug 2543] Bio.Nexus.Trees can't handle named ancestors

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2543





------- Comment #4 from cymon.cox at gmail.com  2008-09-02 10:05 EST -------
Hi Peter,

> Can I ask if you've actually come across trees with names ancestor nodes in
> "real life"?  That would make this bug more important.  If so, the name of the
> tool would be interesting,

P4 (http://code.google.com/p/p4-phylogenetics/) is the only one I'm aware of.

As Frank implies the labels at nodes arent necessarily names of ancestors but
rather are just labels that can be any text. In P4 they are they are just an
string attribute of the node object. P4 uses them primarily to aid tree
drawing. Support indices in phylogenetics are properties of branches and this
is fine in a unrooted tree context. But most systematists want to orientate the
tree, ie. root it informally, and refer to a particular node having the support
value of its subtending branch. Its therefore useful to transfer the branch
support values to node labels before drawing the tree.

> an example tree file would be great to add to
> Biopython as a test case.

How about this:
             +--------------3:t9
      +------2:B
      |      |     +----------------5:t8
      |      +-----4:C
+-----1:A          +---------------6:t4
|     |
|     +---------------7:t6
|
|------------------8:t2
0
|           +------------11:t0
|     +-----10:E
|     |     +-----------------12:t7
|     |
+-----9:D          +------15:t5
      |     +------14:G
      +-----13:F   +-----------------16:t3
            |
            +--------17:t1

"""
#NEXUS

begin taxa;
  dimensions ntax=10;
  taxlabels t0 t1 t2 t3 t4 t5 t6 t7 t8 t9;
end;

begin trees;
  tree random = [&U] (((t9:0.385832, (t8:0.445135,
t4:0.41401)C:0.024032)B:0.041436, t6:0.392496)A:0.0291131, t2:0.497673,
((t0:0.301171, t7:0.482152)E:0.0268148, ((t5:0.0984167,
t3:0.488578)G:0.0349662, t1:0.130208)F:0.0318288)D:0.0273876);
end;
"""

(Hi Frank)

Cheers, Cymon.


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