Q:
I plan to use your program OrthoClust but I am a little confused on the input of the network files. The README just says a list of the nodes; if the first column is node A is the second column a node co-associated with node A?

A:
You are right. A net file is simply what some people call an edgelist. Two numbers in a row form an edge. You can see examples in the data folder found on Github.