Input files

  1. Control file A template control file is used by the python script for submitting BPP jobs.

Create alignments

  1. Create alignments using these four scripts: Uniform Uniform-adaptive Complex Complex-adaptive

Python scripts

To submit BPP jobs use this python script. This script uses a template contro lfile available here.

Parameters:

"-a","--alignmentfolder", help="folder with phylip formatted alignments.", type="string"
"-o","--outputfolder", help="Destination of bpp input files.", type="string"
"-p","--outputfolder2", help="Destination of bpp output files.", type="string"
"--prefix", help="Prefix for naming output files.", type="string"

Example usage:

python python_scripts/run_bpp_heredity_longer_v1a.py -a ./bpp_alignments/ --outputfolder ./bpp_ctl/ --outputfolder2 ./bpp_output/ --prefix nomig_neutral_scaled_1250

Command

The python commands used to run BPP on datasets with a simple genomic architecture are available here.

The python commands used to run BPP on datasets with a complex genomic architecture are available here.

Output files

All alignments are available on Figshare (DOI: 10.6084/m9.figshare.24354277).

The results from BPP runs were summarized using the python script here and results are available here.