All scripts and data necessary to reproduce the analyses in Cascarina and Ross (2020) BMC Genomics are provided in the sub-directories of this repository, along with specific README instructions for each set of analyses.
All analyses require the modified Prion Aggregation Prediction Algorithm (mPAPA.py), located in the separate mPAPA repository. In addition, most scripts rely on multiple external Python packages. For simplicity, it is recommended that you first download and install the appropriate Anaconda distribution at https://www.anaconda.com/distribution/, which automatically includes all necessary dependencies.
mPAPA and all scripts provided in the BMC_Genomics repository are subject to the terms of the GPLv3 license according to license terms of the original PAPA algorithm.