CoNet is a tool that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms). CoNet runs on command line and as a Cytoscape plugin
.You can install CoNet from the Cytoscape App Store or from CoNet's Website where you can also find Tutorials and Documentation