I think (please correct me if I am wrong) that we can't have 1000 for the clade (1 2 3 4 5) since the (1 3 4 5) clade also occurs 28 times. Similary 1, i.e., A, also occurs in two other clades. This means that we can have at most (1000-(28+20+3) = 949) count for the clade (1 2 3 4 5). Is this right? Am I using the wrong function (or with wrong parameters)? Thanks in advance for guidance.
For reference, here is one of the tree (out of 8 unique trees) which occurs 20 times out of 1000, and has A as sibling to only D and E.
Re: Bootstrapping in ape: How to properly use prop.part() and prop.clades() functions to get clade count
My bad! I missed a very basic premise that clade count doesn't (and shouldn't) take the order into account, i.e. (1,2,3,4,5) is same as (1,3,5,4,2) and so one. This means that (1,4,5) and (1,3) are subsets of (1,2,3,4,5), and "obviously" (1,3) isn't a subset of (1,4,5).