How can the user modify ProtoFit to use other speciation models?
Since ProtoFit is Free Software, the user is granted the freedom to modify the source code. Models very similar to models already implemented should be relatively easy to add. Models not very similar may require major modification. This code is designed for legibility and ease of maintenance, however that does not necessarily mean that the code will be easy to understand and modify. It would probably be a good idea for anyone attempting to modify the code to contact the author for advice.