Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
Related Experiment Video
Updated: Aug 28, 2025

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Ethan Kulman1, Jeff Wintersinger2, Quaid Morris1
1Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Abstract:
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).
Related Concept Videos
Phylogenetic Trees
Phylogeny
Evolutionary Relationships through Genome Comparisons
Applications of Molecular Taxonomy
Cancer Survival Analysis
Modern Molecular Taxonomy

