I am currently using ape package to construct genetic trees for my
research, and i am using nj() and mvr() functions
1.i was wondering if there is a way, to create the genetic tree, assuming
that one of the samples, might be an inner node of the tree, and not
necessarily a leaf of the tree (for example, i have samples 1,2,3 and the
tree i want is the 3 being the common father of 1 and 2 that are brothers)
2.when you are using the distance matrix, is there any meaning to the upper
triangle of the matrix?
3.when using mvr, there is a need for variance matrix, i am not using
genetic data, so i can't use the built in genetic functions to get the
variance matrix in the proper format and calculation, is that a simple
variance matrix calculated on the distance values of the distance matrix?
Thanks and best regards.
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