GSR: Editing - CoaSim Simulator

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CoaSim
CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models.
CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. It effectively constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP, micro-satellite, and other haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies. CoaSim is written in C++, Guile Scheme and Python, and is available as source code (under the GNU General Public License, GPL) and as binary versions as Linux RPM files. The source code has been successfully compiled on various Linux and UNIX systems, under OS X and under Windows with Cygwin. As I have only limited access to architectures other than Linux, it is not possible for me to make binary distributions for other platforms, but if anyone is willing to build the distributions I will be more than happy to put them on this site.
4.2.2
10-14-2005
07-11-2011
https://github.com/mailund/CoaSim

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: 16225674], Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L, CoaSim: a flexible environment for simulating genetic data under coalescent models., BMC Bioinformatics, 10-14-2005, https://www.ncbi.nlm.nih.gov/pubmed/?term=16225674,Primary Citation
      [Pubmed ID: 16557026], Liu W, Zhao W, Chase GA, The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests., Hum Hered, 01-01-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16557026,, Application
      [Pubmed ID: 16632491], Mailund T, Schierup MH, Pedersen CN, Madsen JN, Hein J, Schauser L, GeneRecon--a coalescent based tool for fine-scale association mapping., Bioinformatics, 09-15-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16632491,, Application
      [Pubmed ID: 16736029], Bataillon T, Mailund T, Thorlacius S, Steingrimsson E, Rafnar T, Halldorsson MM, Calian V, Schierup MH, The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers., Eur J Hum Genet, 09-01-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=16736029,, Application
      [Pubmed ID: 17042942], Mailund T, Besenbacher S, Schierup MH, Whole genome association mapping by incompatibilities and local perfect phylogenies., BMC Bioinformatics, 10-16-2006, https://www.ncbi.nlm.nih.gov/pubmed/?term=17042942,, Application
      [Pubmed ID: 17346256], Liu W, Yang T, Zhao W, Chase GA, Accounting for genotyping errors in tagging SNP selection., Ann Hum Genet, 07-01-2007, https://www.ncbi.nlm.nih.gov/pubmed/?term=17346256,, Application
      [Pubmed ID: 17550883], Bangham J, Obbard DJ, Kim KW, Haddrill PR, Jiggins FM, The age and evolution of an antiviral resistance mutation in Drosophila melanogaster., Proc Biol Sci, 08-22-2007, https://www.ncbi.nlm.nih.gov/pubmed/?term=17550883,, Application
      [Pubmed ID: 19064712], Besenbacher S, Mailund T, Schierup MH, Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans., Genetics, 02-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19064712,, Application
      [Pubmed ID: 19209719], Pan F, McMillan L, Pardo-Manuel De Villena F, Threadgill D, Wang W, TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees., Pac Symp Biocomput, 01-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19209719,, Application
      [Pubmed ID: 19581452], Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH, Ancestral population genomics: the coalescent hidden Markov model approach., Genetics, 09-01-2009, https://www.ncbi.nlm.nih.gov/pubmed/?term=19581452,, Application
      [Pubmed ID: 21270173], Hobolth A, Dutheil JY, Hawks J, Schierup MH, Mailund T, Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection., Genome Res, 03-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21270173,, Application
      [Pubmed ID: 23284294], Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH, et al., A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species., PLoS Genet, 01-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=23284294,, Application
      [Pubmed ID: 24190946], Munch K, Mailund T, Dutheil JY, Schierup MH, A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion., Genome Res, 03-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24190946,, Application
      [Pubmed ID: 24387001], Yang T, Deng HW, Niu T, Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences., BMC Bioinformatics, 01-03-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24387001,, 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).