NicolaDM
commented
9 months ago The meaning is as follows:
RF This is the number of branches present in one of the two trees but not the other (only branches with length >0.000006 are considered, as often phylogenetic methods use shorter branch lengths to represent effective polytomies; branches shorter than this are considered not present in the trees).
normalised RF This is the RF score divided by the total number of branches in the first tree (including terminal branches). This normalization of the RF score helps to understand how similar two trees are, in a way that does not depend on the size of the trees, so a value of 0.04 would correspond in some sense to a 4% difference between the trees.
Leaves As you would expect.
Found branches This is the number of branches that are found in both the considered trees (again, 0-length or almost-0-length branches are not counted).
Missed branches These are branches in the second tree not found in the first tree.
Not Found Branches Branches in the first tree not found in the second tree.
RFL This is the length-scaled RF distance. It's the sum of abs(l^i_1-l^i_2) where l^i_1 is the length of branch l^i in the first tree and l^i_2 is the length of branch l^i in the second tree. If a branch is not present in a tree, then its length is considered to be 0.
I hope this helps! Let me know if you have further questions.
When calculating the RF distance between several trees, how are the values "found branches", "missed branches", and "not found branches" calculated? If "found branches" is the number of identical branches between the two trees, then what is the difference between branches "missed" and "not found"?