[Bioperl-l] ancestral state derived from Tree

[Ross KK Leung]

By using Tom's advice, I'm able to obtain the distance matrix for the
following tree by Bioperl TreeIO. 

((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000
00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(
L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,
(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000
00);

For the last few nodes T, U and V, they should be monophyletic but U and V
should be more closely related. Although I can use TreeIO methods like
is_monophyletic or is_paraphyletic to test in this case, the problem becomes
more tricky for nodes A, B, C, D because D actually makes no difference from
the common ancestor of nodes A, B, C and D. Since is_monophyletic does not
take into account for this case, is there any workaround? I have to pay
attention to such a detail in order to make a better guess for the ancestral
state(s) at various points of this tree.

Thanks again for the TreeIO developers for making tree analysis easier for
us biologists!