Enumerating and Exploring the Space of Clonal Trees Datasets

This dataset consists of 5 different types of data in 5 different zip files. isa_trees.zip This file contains all single label ISA trees (in newick format) that contain between 1-10 mutations gained. All trees with n mutations gained are located in the sub-directory with the title "newick_n_nodes" (e.g. newick_7_nodes contains all 7 node ISA trees). Each dataset is broken down into several files with names like "newick_7_nodes_start_3_0.txt". Here 7 refers to the number of nodes in the tree, 3 is the identity of the mutation that was first in the corresponding prufer sequence, and 0 indicates which file in the sequence (when the number of trees gets large, the files are broken down so that no more than 1 million trees are contained in each file). cluster_trees.zip This file contains all multi label ISA trees (in newick format) that contain between 2-10 mutations. This dataset does not duplicate the single-label ISA trees (above). The newick format used for these trees uses the delimited "|" between mutations that label the same node. Otherwise, the newick format is the standard format. The files are organized into collections based on the specified number of nodes and number of mutations. Similar to the isa_trees above, the value after "start" in a directory name refers to the starting number in the prufer sequence used to construct the tree topology. The final number in file names refers to which file in the sequence you are considering (when the number of trees gets large, the files are broken down so that no more than 1 million trees are contained in each file). one_deletion_trees.zip This file contains all retricted one-dollo trees (contain exactly one mutation deletion) in newick format that contain between 1-9 mutations gained. Mutation deleteions are indicated using a negative symbol (e.g. -3 means mutation 3 has been deleted). All trees with n nodes (so n-1 mutations gained) are located in the sub-directory with the title "newick_n_nodes". Since the number of mutations gained goes from 1-9, the number of nodes in these trees, range from 2-10. Each dataset is broken down into several files with names like "7_node_deletion_trees_start_5_0.txt". Here 7 refers to the number of nodes in the tree, 5 is the identity of the mutation that was first in the corresponding prufer sequence used to construct the original single-label ISA tree that the deletion was inserted into, and 0 indicates which file in the sequence(when the number of trees gets large, the files are broken down so that no more than 1 million trees are contained in each file). one_dollo_trees.zip This file contains all one-dollo trees (in newick format) that contain between 1-6 mutations gained. Mutation deletions are indicated using a negative symbol (e.g. -3 means mutation 3 has been deleted). All trees with n mutations gained are located in the subdirectory with the title "n_nodes". random_trees.zip This file contains randomly sampled single-label ISA trees using two algorithms: (1) Wilson's algorithm; and (2) an iterative algorithm that randomly selects an existing node to be a parent for each added node (called Psuedorandom in the file). This file contains 1 million randomly sampled trees for each algorithm for 2-10 mutations gained. The trees are included in newick format.