| Input | Description |
|---|---|
| input_file | A tab delimited input file |
| sparsity | A number between zero and one that represents the prior probability that any subclone is absent at any sample, negative values are interpreted as zero |
| num_candidates | Number of initial clusterings to pick for tree analysis |
| maximum_subclones | Maximum number of subclones |
| top_trees | Number of top solutions to show |
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