BRIEF GETTING STARTED:
Use "niche_cluster_run_script.R" to start a simulation of sequences in the overlapping habitats model, compute the distances between simulated sequences, and estimate the ecoSNPs in different genes.

Use "analytical_run_script.R" to estimate the parameters that produce a given population structure as a stationary condition.

COPYRIGHT NOTICE:
The model has been presented in an article:
Marttinen, P. and Hanage, W.P. (2016). Speciation trajectories in recombining bacterial species. Submitted.

You are free to use the code for non-commercial purposes, provided the article above is cited.

Authors make no guarantees about correctness of the code and using the code is done at your own responsibility.

QUESTIONS:
pekka.marttinen@aalto.fi