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Presentation-Ready Data Summary and Analytic Result Tables
post processing of bacterial pangenome gene presence/absence matrices
Infer transmission clusters from SNP and timing data
THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evolution simulation.
Analysis for McLaren, Willis, and Callahan (2019)
This repository contains the algorithms first described in the manuscript that can be accessed under the following DOI: https://doi.org/10.1017/S0031182019000581
Analysis for McLaren, Willis, and Callahan (2019)