Using Tarzan: some hints and problems
More information on how reconstructions are computed and how costs are defined in Tarzan can be found in: Tarzan: Reconstructions and cost model
Note that the cost assigment used in Tarzan and TreeMap differ. E.g. the follwing cost assignment is often used in the literature. In Tarzan the cospeciation are costs -2, duplications costs are 2, sorting costs are 1, and switch costs are 2. This correspond to the cost assignment c=-1 , d=1, s=1, h=1 (switch) of TreeMap.
Some hints and problems when using Tarzan:
1. When there exist too many reconstructions and you use list all reconstructions then Tarzan might hang up itself.
2. It is not possible to change the cost table and the optimization criteria several times in the ReconstructionsViewer. It is always necessary to initialize the ReconstructionsViewer by selecting Build Data Structure in the Tree Editor window before defining a new cost table and new optimization criteria.
3. After listing all reconstructions (or the minimal cost reconstruction) you have to rebuild the the ReconstructionsViewer by selecting Build Data Structure in the Tree Editor to list the minimal cost reconstruction (resp. all reconstructions).
4. For large trees it can happen that edges and vertices exactly overlap.