Scripts

This folder contains python scripts which define the demographic models M1, M2 and M6 models for use with dadi and to convert fasta files into the pseudo_MS format.

Python code for a dadi analysis

The following files can be imported into the main python script which performs the dadi inference.

Python code for converting fasta files into the pseudo_MS format

Usage : python block_cutter_fasta.py 2000 1800 1 *.fa

Here, we are converting a set of aligned fasta files and reading in “2kb” blocks sequentially with an overall tolerance of 200bp of missing information. The 1 signifies that we would like to keep the accepted amount of sequence (which would be at least 1800bp) as a single block for every consecutive stretch of 2kb.

The pseudo_MS files contained in the data folder have been generated with the following command lines.