I'd like to know how frequently topologies are found in a sample of rooted trees, but sumtrees.py seems to return unrooted trees.
I provide an example with trees containing just 4 leaves. sumtrees.py produces the following set of 15 trees, some of which look identical to each other:
TREE Tree1 = [&count=66,probability=0.132,cumulative_probability=0.132](A_2,B_2,(A_1,B_1));
TREE Tree2 = [&count=63,probability=0.126,cumulative_probability=0.258](A_2,B_1,(A_1,B_2));
TREE Tree3 = [&count=57,probability=0.114,cumulative_probability=0.372](A_2,A_1,(B_1,B_2));
TREE Tree4 = [&count=36,probability=0.072,cumulative_probability=0.444](A_2,B_1,(A_1,B_2));
TREE Tree5 = [&count=33,probability=0.066,cumulative_probability=0.51](A_2,B_2,(A_1,B_1));
TREE Tree6 = [&count=29,probability=0.058,cumulative_probability=0.568](A_2,A_1,(B_1,B_2));
TREE Tree7 = [&count=26,probability=0.052,cumulative_probability=0.62](A_2,A_1,(B_1,B_2));
TREE Tree8 = [&count=26,probability=0.052,cumulative_probability=0.672](A_2,B_2,(A_1,B_1));
TREE Tree9 = [&count=26,probability=0.052,cumulative_probability=0.724](A_2,B_1,(A_1,B_2));
TREE Tree10 = [&count=26,probability=0.052,cumulative_probability=0.776](A_2,B_2,(A_1,B_1));
TREE Tree11 = [&count=26,probability=0.052,cumulative_probability=0.828](A_2,B_1,(A_1,B_2));
TREE Tree12 = [&count=24,probability=0.048,cumulative_probability=0.876](A_2,B_2,(A_1,B_1));
TREE Tree13 = [&count=23,probability=0.046,cumulative_probability=0.922](A_2,A_1,(B_1,B_2));
TREE Tree14 = [&count=20,probability=0.04,cumulative_probability=0.962](A_2,B_1,(A_1,B_2));
TREE Tree15 = [&count=19,probability=0.038,cumulative_probability=1.0](A_2,A_1,(B_1,B_2));
Bastien.
My command:
/Downloads/sumtrees.py --rooted --trprobs=/Downloads/treeProbs.txt ~/Downloads/500Trees.txt
The file (shortened, otherwise github won't let me submit an issue; also, the file is properly uploaded, but does not display well in the github issue viewer for some reason. If I click on "edit" I have access to the correct file):
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