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Hi,

Sage uses matplotlib to plot graphs, and valid vertex shapes seem to be valid matplotlib markers, you chan check the matplotlib documentation for some other valid markers.

If you want squares, then you can try, say

sage: g=graphs.PetersenGraph();gp=g.graphplot()
sage: gp.set_vertices(vertex_shape='s');gp.plot()

Apparently changing vertex shapes is still not available for Multi-edged Digraphs though.