note that doing a whole-genome-alignment based synteny analysis may have different strategies to gene (or "marker") based synteny analysis (many of the strategies in that link use the marker based synteny analysis, e.g. aligns the proteins from gene predictions in each genome. see the input data in the table 2). also, depending on the size of your genome (eukaryotic or prokaryote) may affect your choice of synteny tool. similarly, since you are looking at same species, the alignment parameters may be a little different also. aligning genome to genome with minimap2 might be sufficient.