Analyzing bipartite networks in Python

bipy is a Python module to analyse bipartite ecological networks, integrated with NetworkX

Phylogenetic tree classes

PyCoPhy is a set of Python classes to keep track of, and manipulate, very basic phylogenetic trees, with built-in Newick export. It’s designed to be easy to embed in other simulations.

Measuring Ecological Specificity

ESM is a R package to measure ecological specialization at the species level. Most of its functions are included in bipy.