Inference under a spatially-continuous coalescent model (in progress)

Simulation code used for data generation in Inference under a spatially-continuous coalescent model. This is a work in progress.

Dependencies

• Python v2.7
• ERCS v1.0.1: https://pypi.python.org/pypi/ercs
• Discsim v1.0.0: https://pypi.python.org/pypi/discsim
• Arlequin v3.5.1.3: http://cmpg.unibe.ch/software/arlequin35/
• Seq-Gen v1.3.3: http://tree.bio.ed.ac.uk/software/seqgen/

Overview and Setup

The main simulation code is run from simulate.py. Parameter settings are specified in settings.py.

python simulate.py

The script runs simulations as follows:

1. Generate gene trees from Discsim
2. Simulate the corresponding DNA sequences with Seq-Gen
3. Convert the DNA sequences into the appropriate format for Arlequin

Simulation parameters are specified in settings.py. Output sequences are retained use to use with other analytical methods.

The simulation code sets up files for analysis in Arlequin, however Arlequin is not called directly. Instead Arlequin is run as a standalone through their provided scripts. For detailed instruction see the Arlequin manual.

The simulation code expects the compiled program Seq-Gen (named "seq-gen") in the seqgen folder. First download and compile the program from the link above. Rename the compiled program "seq-gen" and place in the folder named "seqgen."

Simulation parameters and random seeds used to run approximate Bayesian computation analysis are saved in the parameters.txt file. The seed used to run the simulation correspond to the names of the files generated for Arlequin.