Open Tree FAQ
Some of these are adapted from the reddit AMA. Others come from the feedback repository. Others are pulled out of thin air.
The synthetic tree does not currently record branch lengths or dates. The tree is constructed by an automated procedure from information found in published phylogenetic trees. These trees rarely have branch lengths or dates. When branch lengths are present, their meaning is variable and it is not clear how one would calibrate them when combining trees. (JAR)
How do I see to a tree depth greater than 3 (if I wanted to capture a screenshot) or switch to a different tree viewer?
We only have the one tree viewer right now, and it is limited to depth of three for performance reasons. The folks behind OneZoom are interested in visualizing our data, and we hope providing the data will perhaps inspire others to build much cooler visualizations than what we have currently on our site. (karen)
For the present we restrict focus to extant lineages. Getting extinct taxa into the tree is definitely high on the priority list! To accomplish this requires two non-trivial tasks: 1) incorporating paleontological taxonomies into our synthetic taxonomy (we’re working on it), and 2) getting a representative sampling of phylogenetic trees into our treestore, which we hope the community will help provide. (josephwb)
A polytomy (node in the synthetic tree that has more than 2 descendant lineages) reflects lack of information rather than implying the simultaneous generation of multiple descendant species. This is either because 1) we have no source trees covering that node, so the resolution comes from taxonomy (which is composed mostly of polytomies), or 2) source trees that touch on the node were unable themselves to provide greater resolution. Such polytomies, especially ones that display only taxonomy, are clear targets for further tree sampling. If you know of trees that can resolve a polytomy, please contribute! (josephwb)
The evolutionary history of life is not really a tree; there is hybridization, lateral gene transfer, endosymbiosis, and so on. Why do you only show a tree?
This is certainly a known limitation of the presentation we’ve chosen (i.e. visualizing the data as a tree rather than a network). The graph database that we use to assemble the synthetic tree allows us to store conflict / different resolutions, and some of that is certainly due to horizontal transfer. So, we have the ability to store that information and we do have plenty of conflicting trees in the data store. The challenge is how to best present & visualize conflict, including how to distinguish between phylogenies that disagree due to different data or methods from a situation where you have identified both horizontal and vertical transfer in the evolutionary history. We'd love to do more in this area. (karen)