Graphical components used in the visualisation of the Pan-Tetris pan-genome matrix. A: Genes are represented by glyphs and build the basis of the matrix. Based on the strand information of the gene, a glyph can either point upwards (gene lies on the forward strand) or downwards (it is on the reverse strand). B: A pan gene, i.e., a group of orthologous genes is shown in a row. The presence and absence of genes, indicated by the presence and/or absence of the respective glyph in each column, reveals which individual genomes share or do not share an ortholog. C: The union of all pan genes constitute the pan-genome. This is represented as a matrix, which shows all pan genes in the rows, and the genomes in the columns. The pan genes are ascendingly ordered based on their appearance in the SuperGenome coordinate system.