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GSR: Simulator - Seq-Gen
| Attribute | Value |
|---|---|
| Title | Seq-Gen |
| Short Description | An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. |
| Long Description | Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution. |
| Version | 1.3.3 |
| Project Started | 2002 |
| Last Release | 12 years, 6 months ago |
| Homepage | http://tree.bio.ed.ac.uk/software/seqgen/ |
| Citations | Rambaut A, Grassly NC, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees., Comput Appl Biosci, 06-01-1997 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 03-28-2020 (1477 days ago) |
| Author verification | The 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence, Protein Sequence, |
| Variations | |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | Phylip, |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | Phylip, NEXUS, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Markov DNA Evolution Models, Codon and Amino Acid Models, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | |
| GSR Certification | Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 15
The following 15 publications are selected examples of applications that used Seq-Gen.
2021
Barbera P, Czech L, Lutteropp S, Stamatakis A, SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements., Mol Ecol Resour, 01-01-2021 [Abstract]
Barbera P, Czech L, Lutteropp S, Stamatakis A, SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements., Mol Ecol Resour, 01-01-2021 [Abstract]
2020
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]
Wade T, Rangel LT, Kundu S, Fournier GP, Bansal MS, Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families., PLoS One, 05-15-2020 [Abstract]
Wade T, Rangel LT, Kundu S, Fournier GP, Bansal MS, Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families., PLoS One, 05-15-2020 [Abstract]
Leuchtenberger AF, Crotty SM, Drucks T, Schmidt HA, Burgstaller-Muehlbacher S, von Haeseler A, Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks., Mol Biol Evol, 12-16-2020 [Abstract]
Leuchtenberger AF, Crotty SM, Drucks T, Schmidt HA, Burgstaller-Muehlbacher S, von Haeseler A, Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks., Mol Biol Evol, 12-16-2020 [Abstract]
Firestone SM, Hayama Y, Lau MSY, Yamamoto T, Nishi T, Bradhurst RA, Demirhan H, Stevenson MA, Tsutsui T, Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates., PLoS One, 07-15-2020 [Abstract]
Firestone SM, Hayama Y, Lau MSY, Yamamoto T, Nishi T, Bradhurst RA, Demirhan H, Stevenson MA, Tsutsui T, Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates., PLoS One, 07-15-2020 [Abstract]
Silva P, Galaverni M, Ortega-Del Vecchyo D, Fan Z, Caniglia R, Fabbri E, Randi E, Wayne R, Godinho R, Genomic evidence for the Old divergence of Southern European wolf populations., Proc Biol Sci, 07-29-2020 [Abstract]
Silva P, Galaverni M, Ortega-Del Vecchyo D, Fan Z, Caniglia R, Fabbri E, Randi E, Wayne R, Godinho R, Genomic evidence for the Old divergence of Southern European wolf populations., Proc Biol Sci, 07-29-2020 [Abstract]
Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN, Estimating effective population size changes from preferentially sampled genetic sequences., PLoS Comput Biol, 10-12-2020 [Abstract]
Karcher MD, Carvalho LM, Suchard MA, Dudas G, Minin VN, Estimating effective population size changes from preferentially sampled genetic sequences., PLoS Comput Biol, 10-12-2020 [Abstract]
Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A, An investigation of irreproducibility in maximum likelihood phylogenetic inference., Nat Commun, 11-30-2020 [Abstract]
Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A, An investigation of irreproducibility in maximum likelihood phylogenetic inference., Nat Commun, 11-30-2020 [Abstract]