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["Supplementary file S5","A","Clustering information obtained at all possible threshold levels for the background dataset (n=1230 genomes) using the novel cgMLST schema with single-linkage hierarchical clustering (HC) algorithm. This file is necessary to implement a nomenclature system with ReporTree, including the three-level hierarchical nomenclature code as used for genogroup definition in this study."]
[null,"B","Clustering information obtained at all possible threshold levels for the background dataset (n=1230 genomes) using the novel cgMLST schema with the GrapeTree MSTreeV2 (GT) algorithm. This file is necessary to implement a nomenclature system with ReporTree, including a three-level hierarchical nomenclature code similar to the genogroup strategy used in this study for HC."]
[null,"C","Clustering information obtained at all possible threshold levels for the background dataset (n=1230 genomes) using the local implementation of PubMLST schema with single-linkage hierarchical clustering (HC) algorithm."]
[null,"D","Clustering information obtained at all possible threshold levels for the core genome alignment of the 53 complete assemblies using single-linkage hierarchical clustering (HC) algorithm."]
[null,"E","Clustering information obtained at all possible threshold levels for the background dataset (n=1230 genomes) using Parsnp with single-linkage hierarchical clustering (HC) algorithm."]
[null,"F","Inter-pipeline corresponding points determined at a CS ≥ 2.85. The column \"method2\" corresponds to the threshold with highest CS to \"method1\". If the flag \"_rev\" is not indicated in the \"comparison\" column, \"method1\" corresponds to the first pipeline indicated. If the flag \"_rev\" is indicated in the \"comparison\" column, \"method1\" is the second pipeline indicated."]

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