RecoPhyNC

RecoPhyNC is a Python software which tests whether a phylogenetic network, given as a file containing a list of arcs, is level-k, tree-child, nearly tree-child, genetically stable, reticulation-visible, tree-sibling, compressed or nearly stable (see the definitions of these classes on the ISIPhyNC website).

RecoPhyNC is a free software under the GPL: you may download it, distribute it and modify it under the same license. Using it requires to install Python as well as the NetworkX library.

Evaluation of properties of phylogenetic networks simulated with the coalescent model with recombination

In their 2008 article entitled Characterization of reticulate networks based on the coalescent with recombination, Arenas, Valiente and Posada generated 14 sets of 1000 phylogenetic networks using the coalescent model with recombination (implemented in the program Recodon) corresponding to different amounts of reticulations, on 10 or 50 leaves.

Using RecoPhyNC, we evaluated the percentage of those networks in several subclasses of phylogenetic networks:

• the detailed results
• a histogram which summarizes the results (note that trees are galled trees, which are tree-child, which are nearly tree-child, which are genetically stable, which are reticulation-visible, which are compressed; also, genetically stable networks are tree-sibling and tree-child networks are nearly stable; more information on ISIPhyNC)