Fig. 1

(A) The workflow of RecView. Solid lines indicate the basic workflow while dashed lines indicate the optional workflow. RecView requires an input genotype file which can be generated by using make_012gt() on the output file from VCFtools. RecView further requires an input scaffold file containing the order and orientation of the scaffolds. These two input files are used together with the built-in dictionary of grandparent-of-origin (GoO) to produce (B) a GoO figure showing the GoO inferences of alleles along the scaffolds, and (E) a figure showing the informative alleles density. RecView can further locate putative recombination positions with the proportional difference or cumulative continuity score algorithms and output (C, D) result figures and (F) tables. The result figures and tables can be saved, including an intermediate table containing the GoO inferences at each SNP