Conclusions
Complete representation of solution space in one figure
Fast solution through dynamic programming
Guarantees global optimality
Correct accounting for host switches
General model, extendable to maximum likelihood
Notes:
Jungles are a complete representation of the solution space of the host/parasite phylogeny reconciliation problem.
Representing the space in this way enables the problem to be solved with dynamic programming, which is REALLY FAST and will find the globally optimal solutions.
Host switching is correctly accounted for with this approach, which was not done in Brooks’ Parsimony Analysis (example? on hand) or in Page’s TreeMap program.
The model is general enough to accommodate maximum likelihood interpretations and allow estimations of actual probabilities of events to be made.