Viral Evolution ReconStructiOn (VERSO)
================
| Branch | Status |
| --- | --- |
| master | [](https://github.com/BIMIB-DISCo/VERSO/actions/workflows/check-bioc.yml) |
| development | [](https://github.com/BIMIB-DISCo/VERSO/actions/workflows/check-bioc.yml) |
In this repository we provide an R implementation of *VERSO*.
*VERSO* is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic
models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints,
by maximizing a log-likelihood function. *VERSO* includes two separate and subsequent steps; in this repository we provide
an R implementation of VERSO STEP #1.
The R version of *VERSO* can be installed from Github. To do so, we need to install the R packages *VERSO* depends on and the devtools package.
```r
# install VERSO dependencies
if (!require("ape")) install.packages("ape")
if (!require("Rfast")) install.packages("Rfast")
# install VERSO library
if (!require("devtools")) install.packages("devtools")
library("devtools")
install_github("BIMIB-DISCo/VERSO", ref = "master")
# load VERSO library
library("VERSO")
```
Please feel free to contact us if you have problems running our tool at daniele.ramazzotti1@gmail.com or d.maspero@campus.unimib.it.
