Here you'll find the supplementary information for our protocol "Demystifying Markov Chain Monte Carlo for Pathogen Bayesian Phylodynamics - A Guide for BEAST Best Practices."
The protocol uses the ebola.fasta file in the 02_cleaned_alignment folder. The script (clean_alignments.sh) to produce this file from the raw data is in the scripts folder. The scripts also contains scripts for producing ML tress, plotting output, and running BEAST on a HPC.
The folder ebola_1634265604 contains the output of a BEAST analyses run using the BEAST.sh best practices script.