Installation
About
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.
Citation | cloneRate citation info |
github.com/bdj34/cloneRate | |
bdj34.github.io/cloneRate/ | |
System requirements | GNU make |
Bug report | File report |
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Depends
R | ≥ 3.6.0 |