This is the homepage of CaveDive, a software for inferring clonal expansions in dated phylogenies, and for simulating phylogenies under a clonal expansion model. For basic usage and tutorial please see the vignette.
For a more formal description of CaveDive, see the following paper: https://doi.org/10.1093/sysbio/syab095
Files and scripts required to reproduce results and figures in this
preprint can be found under the branch paper-data, in the directory R.
You can install CaveDive in R using the following command:
devtools::install_github('dhelekal/CaveDive')
Tutorial is available as a vignette
If you need any assistance please contact david.helekal@gmail.com