Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm

Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for clone trees, and visualize clone trees. Pairtree builds clone trees using up to 100 samples from a single cancer with at least 30 subclonal populations. For complete details on the use and execution of this protocol, please refer to Wintersinger et al. (2022). [Display omitted] •Pairtree is a fast and accurate clone tree reconstruction algorithm•Pairtree builds accurate clone trees using up to 30 subclonal populations•Pairtree provides tools to visualize and interpret clone trees Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build clone trees describing the evolutionary history of individual cancers. Using the Pairtree software package, we describe steps to preprocess somatic mutation data, cluster mutations into subclones, search for clone trees, and visualize clone trees. Pairtree builds clone trees using up to 100 samples from a single cancer with at least 30 subclonal populations.