J. Chifman

Identifiability of speciation times under the multispecies coalescent

This paper shows that branch lengths in fixed species trees with three or four taxa are identifiable and develops estimators and a hypothesis test for delimiting species under the coalescent model.

A Phylogenetic Approach to Inferring the Order in Which Mutations Arise during Cancer Progression

This paper introduces a method to infer the order of somatic mutations in cancer progression using noisy single-cell sequencing data and demonstrates its effectiveness through simulations and empirical data.

HyDe: a Python package for genome-scale hybridization detection

HyDe detects hybridization using phylogenetic invariants from genomic data, distinguishing hybrids and gene flow in simulated and empirical datasets.