How should we view the use of the PhyloTree in our algorithms

[andrewdavidsmith]

My thinking is that for our current purpose the PhyloTree is only used once as a tree object (for each tree that we will consider) in order to construct the proper state transitions, and maybe extract branch lengths associated with state transitions.

If this is true, then we should try to keep anything related to a "neighbor" or a "state" separate from the tree itself. These are not associated with general behaviors of the tree, but rather with our specific use of the tree. Keeping this separation would reduce coupling of software components, making them more easily understood, maintained, debugged, and reused in other contexts. I think probably we can have PhyloTree as a first class object, with methods corresponding to natural and general behaviors, while still having it work just as efficiently when we use it to try and get state transition information. But I'm not completely sure. @jqujqu do you have any thoughts on this?