The title says it all: does anybody know a source for a phylogenetic tree that contains as many completely sequenced eukaryotes as possible (and not too many other species). I do know sources that provide such trees for subgroups (filamentous fungi or green plants and such) and also 'giant trees' with thousands of species.
I would imagine that I am not the only one who could use a tree that focusses on species with completely sequence genomes, e.g. for phylogenomic reasoning.
I am aware of the problem that some higher taxa cannot be places with certainty. This isn't really a big problem for my purpose, I could easily live with unresolved multifurcations or even with a collection of several unconnected subtrees. Here is the one that comes closest to what I need (except for the focus on sequenced organisms): skepticwonder.fieldofscience.com
My question focusses more on the fact if there are trees that show the relatioship between most fully-sequence organisms, not just a few representative members.
I am also aware of the problem that some sequences species are very closely related (which would require a finely resolved tree to separate them) while other eukarytotic groups are sparsely sampled. If I were to draw such a tree, I would probably give up on the high resolution but print multiple species names at the terminal nodes of the low-resolution tree.
Re your edit: I edited my answer :)
and another edit to my answer :)