KIVELA, M., ARNAUDHAOND, S., & SARAMAKI, J. (2015). EDENetworks: A userfriendly software to build and analyse networks in biogeography, ecology and population genetics. Molecular Ecology Resources, 15(1), 117–122.
Résumé: The recent application of graphbased network theory analysis to biogeography, community ecology and population genetics has created a need for userfriendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easytouse interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as BrayCurtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.
