Scripts and simulated data associated with the manuscript "Reference genome choice and filtering thresholds jointly influence phylogenetic analyses". Scripts can also be found at https://github.com/jessicarick/refbias_scripts, but were archived here at the time of manuscript submission. refbias_scripts-preprint.tar.gz contains scripts from GitHub repository simphy_trees.tar.gz contains simulated species trees sim_results_raxml_astral.tar.gz contains trees and tree statistics for simulation analyses emp_results_raxml_astral.tar.gz contains trees and tree statistics for empirical analyses simulation_vcfs.tar.gz contains filtered VCFs that were used for inferring phylogenies