GSR: Simulator - FAVITES
Attribute | Value |
---|---|
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 | 3 years, 6 months ago |
Homepage | https://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 Certification | ✔ Accessibility |
Last evaluated | 02-25-2021 (1121 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Haploid DNA Sequence, RNA, Sequencing Reads, |
Variations | |
Simulation Method | Standard Coalescent, Exact Coalescent, Forward-time, Phylogenetic, Other, |
Input | |
Data Type | Empirical, Ancestral Sequence, |
File format | Program Specific, Other, |
Output | |
Data Type | Genotype or Sequence, Demographic, |
Sequencing Reads | Illumina, Roche 454, SOLiD, IonTorrent, PacBio, Nanopore, Other, Other, |
File Format | Fasta or Fastq, Program Specific, Other, |
Sample Type | Random or Independent, |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, User Defined, |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | |
Mutation Models | Markov DNA Evolution Models, Stepwise Mutation Model, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites, Others, |
Events Allowed | Varying Genetic Features, |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, Others, |
Language | C or C++, Java, R, Python, Perl, Other, |
License | GNU Public License, |
GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 6
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]