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Fig. 1 | BMC Genomics

Fig. 1

From: GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

Fig. 1

An overall workflow of function findPhysLink. In this flowchart, cylinders denote both the input WGS data and a non-redundant (namely, with no sequence duplication) reference database of acquired genes; rounded rectangles denote two key outputs — an association network and a linkage network when reliable APDs are provided; ordinary rectangles denote intermediate results, which are matrices or tables; each arrow represents a process of specific data analysis, which starts from the input and ends at its outcome, with the process name labelled besides the line. Steps integrated into function findPhysLink are encircled by the dashed rectangular border. Abbreviations: cgSNPs, core-genome single-nucleotide polymorphisms (SNPs), which are restricted to biallelic SNPs present in all isolates for GeneMates; PAM: a binary presence-absence matrix

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BMC Genomics

ISSN: 1471-2164

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