[Nauty] help request

clément galan clement.galan at cri-paris.org
Fri Apr 9 03:02:20 AEST 2021

Hello nauty users community,

I'm a bioinformatics student in my first Master's year, currently doing an
internship in a computational biology lab. My project is about generating
an atlas of regulatory networks (i.e. graphs) on which we define ODE
dynamics and then study their behaviour. To this end, we want to create
'all' graphs of a certain size. The graphs that we are considering are all
the non isomorphic, directed and bicolored graphs with 4 vertices,
including loops. Here is an example of the type of graph, as an adjacency
matrix, that we aim to have (edges can take two values, 1 and -1):
[image: image.png]
After reading the documentation, I assumed that to use the nauty package
was the most efficient way to generate all the graphs. However, I
encountered some difficulties to correctly use the nauty / gtools
functions, since my knowledge is still limited in this field. I would
really appreciate if someone could give me indications to tackle my

Best regards,

Clément Galan
CRI Paris and Inria Lyon
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