Genepop support is actually 2 things: The support for the file format, the de facto standard in frequency analysis in population genetics and the support for the application itself.
The current implementation of the parser reads the whole file to a memory structure. This might not be acceptable for very big files with thousands of individuals and thousands of loci. An iterator version is under construction.
The parser is strict regarding the format (i.e., the individual identifier is expected to terminate in a comma). Some applications are less strict, but there is no intention for now to support a relaxed version of the specification.
According to the specification, the last individual of each population is also the subpopulation identifier. This is not great design and in reality users many times forget this. As such the expectation that the last individual id is the subpopulation id many times does not happen.
Two interfaces are supplied: A general, more complex and more efficient one (GenePopController) and a simplified, more easy to use, not complete and not so efficient version (EasyController)