Fig. 1.

Overview of Scoary workflow. The main input files are one genotype and one phenotype matrix and optionally a phylogenetic tree that will define sample genealogy. If the latter is not provided it is calculated internally through the isolate Hamming distances of the input genotype file. Each candidate variant goes through a set of filtration steps, the thresholds for each set by the user. Fewer and fewer candidate variants will be left to analyze as the computational complexity of operations increase. Variants that pass all filters are returned as results