Graphical user interface of Pan-Tetris. The visualisation after a small pan-genome matrix (see additional file S1) has been loaded is shown. The upper left overview panel serves as an orientation map. The red outlined rectangle indicates which part of the complete matrix is loaded in the current view. Next to it the central pan-genome matrix visualisation is seen. Genes of a strain that are present in the respective pan gene group are shown by a glyph that either points upwards if the gene is on the positive strand and/or downwards if it resides on the negative strand. The column next to the pan-genome matrix visualisation is the colour encoding of the pan gene's group size, where core genes are coloured blue, orphans are coloured red and the size of the dispensable pan gene group is encoded by a gradient. The bottom panels are reserved for pan-gene annotations (left), gene annotation (middle) and summary statistics of the complete pan-genome loaded. Two rows have been selected in this example with the respective information shown in the left bottom panel, and one gene whose detailed information is shown in the middle bottom panel. The settings panel at the right allows the user to quickly change appearance of glyph sizes and colour encodings of the graphical elements.