data and scripts for running pySEER on C. difficile dataset
cdiff_CFML_similaritiesMixed.tsv: similarity matrix based on phylogenetic distances filtered_all_hurdle_renamed.vcf: all variants from whole genome alignment to be tested filtered_metadata.txt: metronidazole resistance phenotypes run_pyseer.sh: command used to run pySEER cdiff_snps_mixedModel.txt: output of pySEER with p-values for each SNP in test for assocation with HMR snp_patterns.txt: SNP patterns output by pySEER, used to calculate significance threshold