EDEN: Evolutionary Dynamics within Environments

EDEN corrects for multiple testing, as in the protein group comparisons. Each window with a corrected significant P value (p <0.05 by default) and a mean gap ratio in this window lower than 60% (by default) is reported, where overlapping windows are merged into clusters. For each gene family, EDEN creates a visualization of the dN/dS ratio within the MSA (Fig. 1c). If groupings of samples are provided, EDEN furthermore produces plots allowing differential dN/dS analyses for protein families across these groups. Once the analysis is completed, the user can access and visualize the results via a web browser using a local RStudio Shiny application deployed inside the Docker image. An exemplary output is provided at http://eden.bifo.helmholtz-hzi.de.