upgmanotes.txt

create and write/type outline

break into pieces if necessary

explore and test those pieces, ie, how take the some of all cross-products of uneven size matrices?


#of clusters = N (in an NxN matrix). 
keep track of nodes to assign by initializing them, saving them in a list/graph(by cluster), and indexing them later.
You are not removing anything from this graph, because these are leaves. you are only building initernal nodes upward
find minimum element in the matrix (this is distance; no computations required)
remove selected clusters from the matrix, and replace with the root (set as mean value). 
set the distances of the root to be equal to the mean of the distnaces in the clusters (to all other clusters)
build the subtree with limb-lengths D/2 connected root two the two clusters. 

save this root
get the tree by building off this new (smaller) matrix

insects and dinosaurs

do the root-saving by 


(a == a.min()).nonzero()