GSR: Editing - Splatche Simulator

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Long Description (required)

SPLATCHE (for SPatiaL And Temporal Coalescences in Heterogenous Environment) is a program that allows to incorporate the influence of environment in the simulation of migration of a given species from one or several origin(s). In a second phase, the molecular genetic diversity of one or several samples drawn from the simulated species can be generated. Geographic area and environmental information have to be specified by the program user in a series of input files. Basically, the virtual world where migrations take place is constituted by a matrix of demes. Each deme has its own environmental characteristics according to the input files. A coalescent-based approach allows to generate the molecular diversity of any population sample. The molecular data obtained can then be analyzed in order to study the signature of the simulated demographic scenario. The goal of this online manual is to describe the technical aspects of the software SPLATCHE (version 1.1). This manual complements the article from Currat, Ray and Excoffier, published in 2004. Further details on the methodology can also be found in Ray (2003) and Currat (2004). The pdf version of the user manual could also be download there.

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

Attributes

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.

Source From PMID

Summary of Proposed Changes

To Add

To Remove

Current Citations/Applications

[Pubmed ID: 20956243], Ray N, Currat M, Foll M, Excoffier L, SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination., Bioinformatics, 12-01-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20956243,Primary Citation

[Pubmed ID: 35368907], Larsson DJ, Pan D, Schneeweiss GM, Addressing alpine plant phylogeography using integrative distributional, demographic and coalescent modeling., Alp Bot, 01-01-2022, https://www.ncbi.nlm.nih.gov/pubmed/?term=35368907,, Application

[Pubmed ID: 35931723], Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, et al., Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis., Sci Rep, 08-05-2022, https://www.ncbi.nlm.nih.gov/pubmed/?term=35931723,, Application