Michel Petitjean1, Anne Vanet. 1. Department of Biology, Univ Paris Diderot, Sorbonne Paris Cité, MTI, INSERM UMR-S 973, CNRS, UMR7592, Institut Jacques Monod, F-75013 Paris and Atelier de Bio Informatique, F-75005 Paris, France.
Abstract
SUMMARY: Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists. AVAILABILITY AND IMPLEMENTATION: Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
SUMMARY: Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists. AVAILABILITY AND IMPLEMENTATION: Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
Authors: Abbas Jariani; Christopher Warth; Koen Deforche; Pieter Libin; Alexei J Drummond; Andrew Rambaut; Frederick A Matsen Iv; Kristof Theys Journal: Virus Evol Date: 2019-03-08