Fig. 2

Toy example of OncoNEM inference steps. Given the observed genotypes and the input parameters α and β, the log-likelihood of the start tree, which is by default a star-shaped tree, is −47.61. In the first step of the initial search, all neighbors of the star tree are scored. The highest scoring tree obtained in this step has a log-likelihood of −34.26. In this toy example, the highest scoring tree of the first step is also the best cell lineage tree, overall. Therefore, the initial search terminates with this tree as a solution. In the first refinement step, we find that inserting an unobserved node into the branch point of our current tree increases the log-likelihood by 3.82. Since this improvement is larger than the Bayes factor threshold of 2.3, the solution with the unobserved clone is accepted. In the final refinement step, cells are clustered along edges. In the toy example, only one clustering step does not decrease the log-likelihood by more than log(ε)