| add_noise | Add noise to the VAF values in an F matrix | 
| B_mats | A set of 10 trios of B matrices for experimenting with the methods of 'GeRnika' | 
| B_to_phylotree | Create a 'Phylotree' object from a 'B' matrix. | 
| combine_trees | Get consensus tree between two phylogenetic trees | 
| create_B | Create tumor phylogenetic tree topology | 
| create_F | Calculate the variant allele frequency (VAF) values in a set of samples | 
| create_instance | Create a tumor phylogenetic tree instance | 
| create_phylotree | Create a 'Phylotree' object | 
| create_U | Calculate tumor clone frequencies in samples | 
| equals | Check if two phylogenetic trees are equal | 
| find_common_subtrees | Find the set of common subtrees between two phylogenetic trees | 
| palettes | Palettes for the methods of 'GeRnika' | 
| Phylotree-class | S4 class to represent phylogenetic trees. | 
| plot | Plot a Phylotree object. | 
| plot-method | Plot a Phylotree object. | 
| plot_proportions | Plot a phylogenetic tree with proportional node sizes and colors |