Viral Evolution ReconStructiOn (VERSO)

Branch Status
master R-CMD-check-bioc
development R-CMD-check-bioc

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.

# 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 or .