Once the distance matrix is calculated for the data set, Gene Cluster Family (GCF) assignment is performed for every cutoff distance selected by the
The interactive visualization of BiG-SCAPE output will show the one with the largest number.
For every cutoff, Affinity Propagation will be performed on every subconnected component (BGC) of the distance graph with lower or equal distance to the current cutoff value. Gene Cluster Clan (GCC) setting (enabled by default) will perform a second layer of clustering on the GCFs using the same procedure as before (i.e. on a network of subconnected components) but network nodes will represent GCFs (defined at the cutoff level specified in the first value of the
--clan_cutoff parameter. Default: 0.3). Clustering will be applied to all GCFs connected by a distance lower or equal than the GCC cutoff (the second value of the
--clan_cutoff parameter. Default: 0.7). Inter-GCF distance is calculated as an average distance between the BGCs of both families.
Affinity propagation parameters used in both clustering layers: