Codebase and data related to "High Precision Binary Trait Association on Phylogenetic Trees"

This dataset contains the synthetic and empirical genomic data used to validate and demonstrate SimPhyNI (Simulated Phylogenetic Null Interactions), a framework for high-precision microbial Genome-Wide Association Studies (mGWAS) on binary traits. The data provided supports the paper’s findings regarding SimPhyNI’s ability to achieve near-zero false positive rates and high recall for both positive and negative trait associations in bacteria. The repository includes: Synthetic Validation Datasets: Binary trait matrices and corresponding phylogenetic trees used to benchmark SimPhyNI against existing methods (e.g., Pagel’s correlation, FaST-LMM, TreeWAS). These datasets include simulated "true" (both positive and negative) and neutral associations. Phage Defense System Interaction Data: A binary matrix of phage defense system presence/absence identified across a collection of Escherichia coli genomes from a prior publication. This data was used to identify synergistic and antagonistic relationships between defense mechanisms. E. coli Pangenome Association Analysis: Output files and downstream analysis of a pangenome-wide study of E. coli using a representative set of 500 genomes and over 9 million gene-gene association tests Mycobacterium tuberculosis Antibiotic Resistance Analysis: Output files and comparison of methods for recovering known causal antibiotic-reistance variants in MTB.