| adjl_from_adjmat | From adjacency matrix to adjacency list |
| adjl_from_progindex | Build the network from the already processed Progress Index... |
| campari | Original campari run |
| contract_mst | Compute the contraction of the leaves in the minimum spanning... |
| gen_annotation | Compute the annotation of the progrex index |
| gen_progindex | Compute the progress index along with parent and... |
| mst_from_trj | Create the minimum spanning tree from time series |
| sapphire_plot | Sapphire plot - plotting annotation and progrex index |
| write.pdb.d | Writing a pdb file from trajectory matrix in R |
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