GSR: Simulator - FAVITES

Basic Package Attributes
Short Description FrAmework for VIral Transmission and Evolution Simulation
Long Description FAVITES (FrAmework for VIral Transmission and Evolution Simulation) is a robust modular framework for the simultaneous simulation of a transmission network and viral evolution, as well as simulation of sampling imperfections of the transmission network and of the sequencing process (Moshiri et al., 2018). The framework is robust in that the simulation process has been broken down into a series of interactions between abstract module classes, and the user can simply plug in each desired module implementation (or implement one from scratch) to customize any stage of the simulation process.
Keywords viral, epidemic, phylogeny, evolution, tree, sequence, transmission, contact, network, simulation, stochastic
Version 1.2.7
Project Started 2018
Last Release 5 months, 1 week ago
Citations Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S, FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences., Bioinformatics, 06-01-2019 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified


Last evaluated02-25-2021 (8 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Type of Simulated DataHaploid DNA Sequence, RNA, Sequencing Reads,
Simulation MethodStandard Coalescent, Exact Coalescent, Forward-time, Phylogenetic, Other,
Data TypeEmpirical, Ancestral Sequence,
File formatProgram Specific, Other,
Data TypeGenotype or Sequence, Demographic,
Sequencing ReadsIllumina, Roche 454, SOLiD, IonTorrent, PacBio, Nanopore, Other, Other,
File FormatFasta or Fastq, Program Specific, Other,
Sample TypeRandom or Independent,
Trait Type
Evolutionary Features
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined,
Gene Flow
Life Cycle
Mating System
Natural Selection
Mutation ModelsMarkov DNA Evolution Models, Stepwise Mutation Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others,
Events AllowedVarying Genetic Features,
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris, Others,
LanguageC or C++, Java, R, Python, Perl, Other,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 6 publications are selected examples of applications that used FAVITES.


Sledzieski S, Zhang C, Mandoiu I, Bansal M, TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference, Biocomputing 2021, 01-01-2020 [Abstract]

Dhar S, Zhang C, Mandoiu I, Bansal MS, TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity, ISBRA 2020, 08-18-2020 [Abstract]

Reimering S, Muñoz S, McHardy AC, Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic., PLoS Comput Biol, 02-07-2020 [Abstract]

Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P, The emergence of SARS-CoV-2 in Europe and North America., Science, 10-30-2020 [Abstract]

Moshiri N, Smith DM, Mirarab S, HIV Care Prioritization using Phylogenetic Branch Length., J Acquir Immune Defic Syndr, 12-24-2020 [Abstract]


Balaban M, Moshiri N, Mai U, Jia X, Mirarab S, TreeCluster: Clustering biological sequences using phylogenetic trees., PLoS One, 08-22-2019 [Abstract]

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