A Summary of Available Cophylogeny Software

In general, it may be desirable to use multiple software tools for cophylogeny reconstruction analyses. Jane complements other cophylogeny software tools such as TreeMap (using the Jungles method) and CoRe-PA. A brief comparison of the software packages is included below.

Software	Advantages	Disadvantages	Features
Jane 3	Fast and guarantees correct solutions User controls trade-off between running time and quality of solutions Tested with trees with over 200 tips	Optimal solution not guaranteed	Interactive solution viewer Failure to diverge events Preferential host switching mechanisms Statistical analysis tool
TreeMap	Always gives optimal solutions	Exponential worst-case running time prohibitive for large trees	Finds Pareto-optimal solution set
CoRe-PA	Fast Automatic selection of cost parameter values Many user-configurable options	Optimal solution not guaranteed Sometimes reports temporally inconsistent solutions	Graphical tree-drawing interface Statistical analysis tool

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