| Factory | Module to sequentially generate Phylogenetic Networks |
| FactoryX | Module to sequentially generate Phylogenetic Networks |
| GraphViz | Interface between PhyloNetwork and GraphViz |
| RandomFactory | Module to generate random Phylogenetic Networks |
| TreeFactory | Module to sequentially generate Phylogenetic Trees |
| TreeFactoryMulti | Module to sequentially generate Phylogenetic Trees |
| TreeFactoryX | Module to sequentially generate Phylogenetic Trees |
| muVector | Module to compute with vectors of arbitrary dimension |