GSR: Editing - msms Simulator

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msms
A coalescent Simlation tool with selection.
This document describes how to use msms, a tool to generate sequence samples under both neutral models and a single locus selection model. msms permits the full range of demographic models provided by ms(Hudson, 2002). In partic-ular, it allows for multiple demes with arbitrary migration patterns, population growth and decay in each deme, and for population splits and mergers. Selection (including dominance) can depend on the deme and also change with time. The program is designed to be command line compatible to ms, however no prior knowledge of ms is assumed for this document. Applications of this program include power studies, analytical comparisons, approximated Bayesian computation among many others. Because most applications require the generation of a large number of independent replicates, the code is designed to be efficient and fast. For the neutral case, it is comparable to ms and even faster for large recombination rates. For selection, the performance is only slightly slower, making this one of the fastest tools for simulation with selection. The program has been developed with a wide number of possible operating systems and hardware in mind. For this reason, the code has been developed in Java and can run on any hardware that supports Java 1.6. This includes Mac OS X, all current versions of MS Windows, and most Unix flavors (Linux, Sun, BSD). The Java programing language is also popular and widely known which should facilitate the writing of extensions for the program.
3.2rc-b75
11-07-2010
11-07-2010
http://www.mabs.at/ewing/msms/index.shtml

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: 664655], Wetrich RM, Sidhu DS, Giant sigmoid diverticulum., West J Med, 06-01-1978, https://www.ncbi.nlm.nih.gov/pubmed/?term=664655,, Application
      [Pubmed ID: 20591904], Ewing G, Hermisson J, MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus., Bioinformatics, 08-15-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20591904,Primary Citation
      [Pubmed ID: 29569384], Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, Martin SH, Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography., Mol Ecol, 10-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29569384,, Application
      [Pubmed ID: 29608730], Bitarello BD, de Filippo C, Teixeira JC, Schmidt JM, Kleinert P, Meyer D, Andrés AM, Signatures of Long-Term Balancing Selection in Human Genomes., Genome Biol Evol, 03-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29608730,, Application
      [Pubmed ID: 29723195], Key FM, Abdul-Aziz MA, Mundry R, Peter BM, Sekar A, D'Amato M, Dennis MY, Schmidt JM, Andrés AM, Human local adaptation of the TRPM8 cold receptor along a latitudinal cline., PLoS Genet, 05-03-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29723195,, Application
      [Pubmed ID: 29866176], Wang J, Ding J, Tan B, Robinson KM, Michelson IH, Johansson A, Nystedt B, Scofield DG, Nilsson O, Jansson S, et al., A major locus controls local adaptation and adaptive life history variation in a perennial plant., Genome Biol, 06-04-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29866176,, Application
      [Pubmed ID: 30364947], Hartasánchez DA, Brasó-Vives M, Heredia-Genestar JM, Pybus M, Navarro A, Effect of Collapsed Duplications on Diversity Estimates: What to Expect., Genome Biol Evol, 11-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=30364947,, Application
      [Pubmed ID: 30451848], vonHoldt BM, Kartzinel RY, Huber CD, Le Underwood V, Zhen Y, Ruegg K, Lohmueller KE, Smith TB, Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus., Nat Commun, 11-19-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=30451848,, 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).