GSR: Simulator - Seq-Gen

Basic Package Attributes
AttributeValue
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 9 years ago
Homepagehttp://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 ]
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Last evaluated03-28-2020 (202 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
Target
Type of Simulated DataHaploid DNA Sequence, Protein Sequence,
Variations
Simulation MethodPhylogenetic,
Input
Data TypeAncestral Sequence,
File formatPhylip,
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatPhylip, 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 ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Heterogeneity among Sites,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
License
GSR CertificationDocumentation, Support,

The following 1 publications are selected examples of applications that used Seq-Gen.

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]


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