GSR: Editing - Seq-Gen Simulator

You may request changes to this simulator by navigating to the Basic, Details, and Citations/Applications tabs. When you are finished, open the Submit tab. To return back to the simulator view, click Seq-Gen. Finally, please take note of the GSR simulator privacy policy.
Seq-Gen
An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees.
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.
1.3.3
12-04-2002
10-18-2011
http://tree.bio.ed.ac.uk/software/seqgen/
None

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.

Every sub-attribute is selected
Not all sub-attributes are selected
  • Target
    • Type of Simulated Data
      • Genotype at Genetic Markers
      • Diploid DNA Sequence
      • Haploid DNA Sequence
      • RNA
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
    • Variations
      • Biallelic Marker
      • Multiallelic Marker
      • Single Nucleotide Variation
      • Amino acid variation
      • Microsatellite
      • Insertion and Deletion
      • CNV
      • Inversion and Rearrangement
      • Alternative Splicing
      • Missing Genotypes
      • Genotype or Sequencing Error
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Other
  • Input
    • Data Type
      • Allele Frequencies
      • Empirical
      • Ancestral Sequence
      • Saved simulation
      • Reference genome
      • Other
    • File format
      • Arlequin
      • CREATE
      • Fstat
      • GDA
      • Genepop
      • MIGRATE
      • MS
      • SAM or BAM
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Demographic
      • Mutation
      • Methylation
      • Gene Expression
      • Protein Expression
      • Linkage Disequilibrium
      • Diversity Measures
      • Fitness
      • Sequencing Reads
        • Illumina
        • Roche 454
        • SOLiD
        • IonTorrent
        • PacBio
        • Nanopore
        • Other
      • Other
    • File Format
      • Arlequin
      • Fasta or Fastq
      • Fstat
      • Genepop
      • Linkage
      • MIGRATE
      • MS
      • PED
      • Phylip
      • NEXUS
      • STRUCTURE
      • VCF
      • SAM or BAM
      • Tree Sequence
      • Program Specific
      • Other
    • Sample Type
      • Random or Independent
      • Sibpairs, Trios and Nuclear Families
      • Extended or Complete Pedigrees
      • Case-control
      • Longitudinal
      • Other
  • Phenotype
    • Trait Type
      • Binary or Qualitative
      • Quantitative
      • Multiple
    • Determinants
      • Single Genetic Marker
      • Multiple Genetic Markers
      • Sex-linked
      • Gene-Gene Interaction
      • Environmental Factors
      • Gene-Environment Interaction
  • Evolutionary Features
    • Demographic
      • Population Size Changes
        • Constant Size
        • Exponential Growth or Decline
        • Logistic Growth
        • Bottleneck
        • Carrying Capacity
        • User Defined
      • Gene Flow
        • Stepping Stone Models
        • Island Models
        • Continent-Island Models
        • Sex or Age-Specific Migration Rates
        • Influenced by Environmental Factors
        • Admixed Population
        • User-defined Matrix
        • Other
      • Spatiality
        • Discrete Models
        • Continuous Models
        • Landscape Factors
    • Life Cycle
      • Discrete Generation Model
      • Age structured
      • Overlapping Generation
      • User-Defined transition matrices
    • Mating System
      • Random Mating
      • Monogamous
      • Polygamous
      • Haplodiploid
      • Selfing
      • Age- or Stage-Specific
      • Assortative or Disassortative
      • Other
    • Fecundity
      • Constant Number
      • Randomly Distributed
      • Individually Determined
      • Influenced by Environment
      • Other
    • Natural Selection
      • Determinant
        • Single-locus
        • Multi-locus
        • Codon-based
        • Fitness of Offspring
        • Phenotypic Trait
        • Environmental Factors
      • Models
        • Directional Selection
        • Balancing Selection
        • Multi-locus models
        • Epistasis
        • Random Fitness Effects
        • Disruptive
        • Phenotype Threshold
        • Frequency-Dependent
        • Other
    • Recombination
      • Uniform
      • Varying Recombination Rates
      • Gene Conversion Allowed
    • Mutation Models
      • Two-allele Mutation Model
      • Markov DNA Evolution Models
      • k-Allele Model
      • Infinite-allele Model
      • Infinite-sites Model
      • Stepwise Mutation Model
      • Codon and Amino Acid Models
      • Indels and Others
      • Heterogeneity among Sites
      • Others
    • Events Allowed
      • Population Merge and Split
      • Varying Demographic Features
      • Population Events
      • Varying Genetic Features
      • Change of Mating Systems
      • Other
    • Other
      • Phenogenetic
      • Polygenic background
  • Interface
    • Command-line
    • Graphical User Interface
    • Integrated Development Environment
    • Script-based
    • Web-based
  • Development
    • Tested Platforms
      • Windows
      • Mac OS X
      • Linux and Unix
      • Solaris
      • Others
    • Language
      • C or C++
      • Java
      • R
      • Python
      • Perl
      • Visual Basic
      • Other
    • License
      • GNU Public License
      • BSD
      • Creative Commons
      • MIT
      • Other
  • GSR Certification
    • Accessibility
    • Documentation
    • Application
    • Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

    To Remove

      Can't Find the Attribute You Are Looking For?

      If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

      You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

      Summary of Proposed Changes

      To Add

      To Remove

      Current Citations/Applications

      [Pubmed ID: 9183526], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=9183526,Primary Citation
      [Pubmed ID: 32032362], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32032362,, Application
      [Pubmed ID: 32413061], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32413061,, Application
      [Pubmed ID: 32413061], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32413061,, Application
      [Pubmed ID: 32637998], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32637998,, Application
      [Pubmed ID: 32637998], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32637998,, Application
      [Pubmed ID: 32667952], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32667952,, Application
      [Pubmed ID: 32667952], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32667952,, Application
      [Pubmed ID: 32693716], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32693716,, Application
      [Pubmed ID: 32693716], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32693716,, Application
      [Pubmed ID: 32996237], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32996237,, Application
      [Pubmed ID: 32996237], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=32996237,, Application
      [Pubmed ID: 33044955], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=33044955,, Application
      [Pubmed ID: 33044955], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=33044955,, Application
      [Pubmed ID: 33257660], Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A, An investigation of irreproducibility in maximum likelihood phylogenetic inference., Nat Commun, 11-30-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=33257660,, Application
      [Pubmed ID: 33257660], Shen XX, Li Y, Hittinger CT, Chen XX, Rokas A, An investigation of irreproducibility in maximum likelihood phylogenetic inference., Nat Commun, 11-30-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=33257660,, Application
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      Please inform the GSR team here if you would like to see an attribute added to the attribute tree (or any other changes to the simulator description system as it exists).