[Bioperl-l] ancestral state derived from Tree

Ross KK Leung ross at cuhk.edu.hk
Tue Sep 27 23:57:52 EDT 2011

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


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!

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