A demography and chromosome modeler for coalescent simulations
modeler4simcoal2 (m4s2) is a modeler for coalescent processes. It allows the modeling of both demographies and chromosomes (i.e., markers with linkage relationships in multiple chromosome blocks).
m4s2 generates files for usage with Simcoal2 which can easily be analyzed with Arlequin3. m4s2 can be run standalone or can directly call and control Simcoal2. Arlequin3 can also be called after the simulations are run.
m4s2 is a Java Web Start application (requiring Java 1.4, available for Windows, Mac and Linux among others). It requires no installation and can be run directly from the web. m4s2 can be run on more platforms than those supported by Simcoal2 and Arlequin3 (in this case only in standalone mode)
The purpose of m4s2 is to allow biologists to concentrate more on biology and the underlying models used on analysis (and less on having to learn a new computer simulation tools). We expect that m4s2 will lower the barrier for coalescent simulator use.
m4s2 has full expressive power with regards to chromosome modeling (i.e., it can model all that Simcoal2 supports).
Regarding demographies, m4s2 includes a set of models which cover the vast majority found in the literature (e.g., island, stepping-stone). An extension system is also provided allowing for the creation of new models. A simple extension language is provided, if the language is not enough the full expressive power of Python (Jython) can be used to create new models. New models can be made available online as m4s2 can import those directly from the web. We make available an external model on the expansion of humans and domesticated species after the Neolithic as hierarchically structured.