GSR: Simulator - FAVITES

Basic Package Attributes
AttributeValue
Title FAVITES
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 7 months, 2 weeks ago
Homepagehttps://github.com/niemasd/FAVITES
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

Accessibility
Documentation
Application
Support

Last evaluated02-25-2021 (61 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence, RNA, Sequencing Reads,
Variations
Simulation MethodStandard Coalescent, Exact Coalescent, Forward-time, Phylogenetic, Other,
Input
Data TypeEmpirical, Ancestral Sequence,
File formatProgram Specific, Other,
Output
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,
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined,
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models, Stepwise Mutation Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others,
Events AllowedVarying Genetic Features,
Other
InterfaceCommand-line,
Development
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.

2020

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]

2019

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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