Inferring and Summarizing Tumor Phylogenies from Bulk DNA Data
Sapling is a Python tool for inferring and summarizing tumor phylogenies from bulk DNA data. In addition to identifying full trees, Sapling also identifies "backbone trees" that summarize the space of plausible evolutionary histories. Sapling supports multiple solvers (fastPPM, CVXOPT, Gurobi) to estimate frequency matrices and infer high-likelihood trees.
