It's such a shame that the project website hasn't been updated anymore since '11 due to funding problems. It was a huge help during my studies and I enjoyed just browsing around on it.
If you like this, you should try http://www.onezoom.org/
This is very cool!
But damn, it's complicated. Consider the root. As I vaguely understand it, evolution of eukaryotes involved multiple fusions of separate lines. The basic cell came from one line. And nuclei, mitochondria and chloroplasts from other lines. I gather that there was at first symbiosis, which then became permanent. And perhaps other organelles came from other lines.
Nuclei and mitochondria must have integrated first, because both plants and animals have them. And then plants got chloroplasts.
I wonder whether relationships are clear enough yet to include in the tree.
Great website which I used many times to check the precise species appearing in photos I made. Unfortunately the project seems to have stopped updating over 9 years ago (if the news page is a good indicator).
A summary view that may be of interest:
You can explore the tree of life including extinct branches. It is incredible to see that for each live branch there are many branches that didn't make it.
I have fond memories working on an interactive visualization on a MS Surface table using this data. Great to see TOL still being used!
just found this up-to-date, interactive version of the Tree of Life > http://lifemap.univ-lyon1.fr/