Tree_Mash.nwk: Mash tree in newick format.
Tree_Mash_distances.tab: Mash distance matrix.
Tree_MaximumLikelihood.nwk: Maximum Likelihood consensus tree in newick format.
Tree_Pseudosequences.fa: Pseudosequences as input for Maximum Likelihood tree.
Variants_All_filtered.vcf: Variants (full set) for XGBoost analyis.
Variants_LD_pruned.vcf: Variants for Maximum Likelihood tree and PCA.
Variants_NoMissingAllele.vcf: Variants for Treemix and F4 analysis.
XGB_*.ipynb: Jupyter notebook containing Python code for XGBoost analysis.