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Updated: Jul 26, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
Bingxin Lu1,2, Kit Curtius3,4, Trevor A Graham3,5
1Department of Cell and Developmental Biology, University College London, London, UK. b.lu@ucl.ac.uk.
Abstract:
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation.
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