runDaDi Files

This project includes several python scripts to run demographic analysis for pairs of species or populations with dadi software: https://pypi.org/project/dadi/  This software has to be installed prior to running the python scripts listed on this page.

runDaDi.py code is parallelised to takes advantage of multicore CPUs and multi-CPU machines. 
It controls total CPU load across all cores and CPUs and will not start the next model until CPU load drops below maxCPUload parameter (=90% by default) listed at the beginning of the script.

runDaDi.py is the most recent and still developing. 
Other scripts listed here are older and not supported.
Please use python3 to run these scripts. Under python2 they run, but generate incorrect results.

To run runDaDi.py the user needs to edit a few parameters (file name, sample sizes etc) at the beginning of the file.
To prepare the *.dad data file you can use ProSeq4 (https://sourceforge.net/projects/proseq/ ) to convert from VCF or other widely used formats to the "dadi format". ProSeq4 can be slow to load very large genome-scale VCF files, but once openned (and saved in the native *.df file) it works much faster and does the job well.

Run the script with the command: python runDaDi.py   or  python3 runDaDi.py

All 2D demographic models descriptions are contained in the runDaDi.py. Feel free to modify if needed. 

No warranty of any kind provided. Use at your own risk. Good luck ;)

Citation: 
Filatov D.A. et al (2021) The mode of speciation during a recent radiation in open-ocean phytoplankton. Curr Biol Vol. 31 Issue 24 Pages 5439–5449. DOI: 10.1016/j.cub.2021.09.073