A guide to the literature on network reconstruction. Methodological similar approaches are clustered together by a decision tree built on five basic questions: Do the data contain knock-out or knock-down samples? Is the model deterministic or probabilistic? Does the model account for changes over time or is it static? Does the model focus on transcriptional gene regulation networks? And if so, does the model take additional non-transcriptional effects into account? In the leaf nodes of the tree, a few representative references are shown.