Popular repositories

1. Nestedness

   Scripts to calculate the nested structure of a bipartite matrix and the null models used to test the statistical significance of nestedness.

   MATLAB 1

2. avida_host-parasite

   Configuration files and data set used in the following study: "Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms", published in the speci…

   Shell 1

3. WebOfLife

   Jupyter notebook writen in R to access, download, manipulate, analyze, and plot data on the species interaction networks stored in the Web Of Life database (a kind of API).

   Jupyter Notebook 1 1

4. BirdMigrationNetworks

   Data set and R code used in the following study: "Phylogenetically-conserved bird migration networks determine the distribution of avian flu", which has been recently submitted (2020).

   R 1

5. avida_genbank

   Configuration files and bash scripts used in the following study: "The genotype-phenotype map of an evolving digital organism", published in PLoS Computational Biology (2017).

   Shell

6. coevolutionary_networks_in_the_lab

   Dataset and R code used in the following study: "Coevolutionary dynamics shape the structure of bacteria-phage infection networks", published in Evolution (2019).

   R