New: seqtime is an R package for the analysis of microbial community time series data.

CoNet is a Cytoscape plugin dedicated to the prediction of association networks from objects' presence/absence or abundance data. The objects can be anything from genes to species.

The Network analysis tool suite (NeAT) was jointly developed by Sylvain Brohée and Karoline Faust. These tools are now employed within the MICROME framework.
A command line version of the path finding and pathway inference tools in NeAT can be downloaded from here.