GSR: Editing - ms Simulator

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ms
The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets.
The program ms can be used to generate many independent replicate samples under a variety of assumptions about migration, recombination rate and population size to aid in the interpretation of such polymorphism studies. The samples are generated using the now standard coalescent approach in which the random genealogy of the sample is rst generated and then mutations are randomly place on the genealogy (Kingman, 1982; Hudson, 1990; Nordborg, 2001). The usual small sample approximations of the coalescent are used. An infinitesites model of mutation is assumed, and thus multiple-hits and back mutations do not occur. However, when used in conjunction with other programs, finite-site mutation models or micro-satellite models can be studied. For example, the gene trees themselves can be output, and these gene trees can be used as input to other programs which will evolve the sequences under a variety of finite-site models. These are described later. The program is intended to run on Unix, or Unix-like operating systems, such as Linux or MacOsX. The next section describes how to download and compile the program. The subsequent sections described how to run the program and in particular how to specify the parameter values for the simulations.
20161016
05-29-2002
10-16-2016
http://home.uchicago.edu/~rhudson1/source/mksamples.html

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
      • Gene Expression
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
      • Single-Cell Sequencing
      • Bulk Sequencing
      • Proteomics
      • Chromatin Conformation
    • 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
      • Ionization
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Neural network
    • 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
      • Phylogenetic Tree
      • 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: 11847089], Hudson RR, Generating samples under a Wright-Fisher neutral model of genetic variation., Bioinformatics, 02-01-2002, https://www.ncbi.nlm.nih.gov/pubmed/?term=11847089,Primary Citation
      [Pubmed ID: 29686078], Price N, Moyers BT, Lopez L, Lasky JR, Monroe JG, Mullen JL, Oakley CG, Lin J, Ågren J, Schrider DR, et al., Combining population genomics and fitness QTLs to identify the genetics of local adaptation in <i>Arabidopsis thaliana</i>., Proc Natl Acad Sci U S A, 05-08-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29686078,, Application
      [Pubmed ID: 29746697], Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, et al., Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication., Mol Biol Evol, 07-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29746697,, Application
      [Pubmed ID: 29760079], Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, et al., Selection and environmental adaptation along a path to speciation in the Tibetan frog <i>Nanorana parkeri</i>., Proc Natl Acad Sci U S A, 05-29-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29760079,, Application
      [Pubmed ID: 29899660], Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, et al., Detecting the Population Structure and Scanning for Signatures of Selection in Horses (<i>Equus caballus</i>) From Whole-Genome Sequencing Data., Evol Bioinform Online, 06-04-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29899660,, Application
      [Pubmed ID: 30044798], Fujito NT, Satta Y, Hane M, Matsui A, Yashima K, Kitajima K, Sato C, Takahata N, Hayakawa T, Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia., PLoS One, 07-25-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=30044798,, 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).