Would '--force-rooted' give you what you want?
On 3/29/19 5:40 AM, Alexei Kassian wrote:
> Hi all,
>
> I have a set of trees (e.g., MrBayes output *.runX.t) with many taxa: A,
> B, C, .... Z.
>
> I need to infer statistical support for a certain clade ((E,F),G).
>
> I use the options '--target-tree-filepath=target.tre --force-unrooted'
> and the target.tre with the following content: (A,B,C,...Z,((E,F),G)).
>
> For the clade ((E,F),G), Sumtrees returns the cumulative number of trees
> which contain ((E,F),G), or (E,(F,G)), or (E,F,G).
>
> Is it possible to get a number of trees with the exact clade ((E,F),G)
> without trees with (E,(F,G)) or (E,F,G)?
>
> Thank you in advance.
>
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I can reformulate the problem, since my actual task is somewhat more complicated than the simplest task described in my first message.
I have a poorly resolved 'roaming' taxon Z which skips across the tree, particularly Z can be inserted within the clade E,F,G.
I want to infer probability of my clade ((E,F),G) regardless whether the taxon Z is placed within this clade or not.
To do so, I need to infer:
1) ((E,F),G)
2) ((E,F,Z),G)
3) ((E,F),G,Z)
and some other combinations with Z. And then summarize the obtained values.
Does Sumtrees allow such calculations?
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