pydot is just a python tool to work with the dot graph format, it will
eventually just call dot in the command line.
In this case there's the additional overhead of having pydot parse the
whole input, generate the representation for the graph and then dump
it to a temporary file to be consumed by dot. So as you can see it
will never be even close in speed as compared to simply running dot on
a .dot file directly.
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ero