Question: How to obtain statistical support for a certain hard clade when a set of phylogenetic trees is given?
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gravatar for Alexei Kassian
15 months ago by
Alexei Kassian10 wrote:

I have a set of trees (e.g., MrBayes output *.run1.t, *.run2.t) with many taxa: A, B, C, .... Z.

I need to infer statistical support for a certain clade with the fixed topology ((E,F),G).

Sumtrees (Dendropy package) is a useful tool, but the only thing it can provide in my case is 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) excluding trees with (E,(F,G)) or (E,F,G)?

Thank you in advance.

clade topology • 277 views
ADD COMMENTlink modified 15 months ago by Joe17k • written 15 months ago by Alexei Kassian10
0
gravatar for Joe
15 months ago by
Joe17k
United Kingdom
Joe17k wrote:

You can follow the approach in this previous answer of mine: Detect trees (newick) with specific topology

If you just treat the tree as a string, search exactly for the number of trees containing the string ((E,F), G). You can convert to a cladogram, or use some regex magic to get around the branch lengths and bootstrap values within those clades.

ADD COMMENTlink written 15 months ago by Joe17k
1

Dear Joe, this is indeed an easy and ingenious way, thank you.

ADD REPLYlink written 15 months ago by Alexei Kassian10
1

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

ADD REPLYlink written 15 months ago by genomax85k
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