cloneRate

CRANcloneRateMaRDI QIDQ5981836FDOQ5981836

Estimate Growth Rates from Phylogenetic Trees

Kit Curtius, Brian Johnson, Jason Schweinsberg, Yubo Shuai

Last update: 22 September 2023

Copyright license: MIT license, File License

Software version identifier: 0.2.3

Description

Quickly estimate the net growth rate of a population or clone whose growth can be approximated by a birth-death branching process. Input should be phylogenetic tree(s) of clone(s) with edge lengths corresponding to either time or mutations. Based on coalescent results in Johnson et al. (2023) <doi:10.1093/bioinformatics/btad561>. Simulation techniques as well as growth rate methods build on prior work from Lambert A. (2018) <doi:10.1016/j.tpb.2018.04.005> and Stadler T. (2009) <doi:10.1016/j.jtbi.2009.07.018>.

Cites work

• On incomplete sampling under birth-death models and connections to the sampling-based coalescent
• The coalescent of a sample from a binary branching process
• cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory

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