virHap

PhyVar is an open-source software package for viral quasi-species reconstruction, which makes use of a
novel phyloprobabilistic approach to infer the sub clonal composition and evolutionary history of a viral population
from NGS data. The program aims to characterize and quantify the composition, the abundance and
the evolutionary path of the underlying viral population within a given host by analyzing Next Generation
Sequencing data.
The program takes as input the collection of reads (or several collections of reads in case of many data
samples) and the reference genome and it constructs the evolutionary tree exhibiting the species abundance
profile and the list of haplotypes along with their prevalences.