Within-host adaptive virus evolution sequence simulator.
The goal of wavess is to simulate within-host virus sequence evolution optionally including recombination, a latent infected cell reservoir, and three types of selection (conserved sites, comparison to a fit sequence, and antibody-mediated immunity). The package also provides functions to pre-process data for input into the simulator, as well as post-processing functions to analyze the simulation output. The post-processing functions can also be used on real data. The default settings for the simulator assume that the sequences being simulated are HIV gp120.
Installation
You can install the development version of wavess from GitHub with:
# install.packages("devtools")
devtools::install_github("MolEvolEpid/wavess")This will not install the vignettes locally. If you’d like to install the vignettes locally, you can use the command:
# install.packages("devtools")
devtools::install_github("MolEvolEpid/wavess", build_vignettes = TRUE, force = TRUE)Vignettes
Please see the following vignettes for examples:
- Preparing input data:
vignette("prepare_input_data") - Running wavess:
vignette("run_wavess") - Analyzing the output:
vignette("analyze_output") - Running the python script:
vignette("python")
Contributing
You are of course welcome to fork the package for your own use. If you would like for your changes to be incorporated into the latest version of wavess, please open an issue related to your proposed change, create a pull request with the implemented change, or reach out to tkl@lanl.gov, nsambaturu@binghamton.edu, or zenalapp@lanl.gov.