Best methodology to compare computed phylogeny tree with taxonomy?
Take a look at the ape package in R. It has a function called cophyloplot which allows you to visualize two trees like so:



Which is well described in this question (also the source of the image).

There is also the dist.topo function which produces a metric which describes the topological distance between two phylogenetic trees. I don't know if this is what you mean by "divergent" but I hope it helps.