GSR: Editing - SimPhy 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 SimPhy. Finally, please take note of the GSR simulator privacy policy.
SimPhy
A comprehensive simulator of gene family evolution
SimPhy simulates the evolution of multiple gene families under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible.
Species tree, Gene Tree, Locus Tree, Multispecies coalescent, Incomplete lineage sorting, Gene duplication, Gene loss, Horizontal gene transfer, Lateral gene transfer, Rate heterogeneity
1.0.2
07-01-2015
03-18-2016
https://github.com/adamallo/SimPhy
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
      • Phenotype
    • 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: 26086579], Bayzid MS, Mirarab S, Boussau B, Warnow T, Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses., PLoS One, 06-18-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26086579,, Application
      [Pubmed ID: 26449249], Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T, A comparative study of SVDquartets and other coalescent-based species tree estimation methods., BMC Genomics, 01-01-2015, https://www.ncbi.nlm.nih.gov/pubmed/?term=26449249,, Application
      [Pubmed ID: 26526427], Mallo D, De Oliveira Martins L, Posada D, SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees., Syst Biol, 03-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=26526427,Primary Citation
      [Pubmed ID: 27189547], Sayyari E, Mirarab S, Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies., Mol Biol Evol, 07-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27189547,, Application
      [Pubmed ID: 27480613], Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C, Reversible polymorphism-aware phylogenetic models and their application to tree inference., J Theor Biol, 10-21-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27480613,, Application
      [Pubmed ID: 28113327], Davidson R, Lawhorn M, Rusinko J, Weber N, Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods., IEEE/ACM Trans Comput Biol Bioinform, 05-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=28113327,, Application
      [Pubmed ID: 28185574], Sayyari E, Mirarab S, Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction., BMC Genomics, 11-11-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=28185574,, Application
      [Pubmed ID: 28800608], Mai U, Sayyari E, Mirarab S, Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction., PLoS One, 08-11-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28800608,, Application
      [Pubmed ID: 28835989], Bhattacharyya S, Mukherjee J, IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count., J Mol Evol, 08-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28835989,, Application
      [Pubmed ID: 29029241], Sayyari E, Whitfield JB, Mirarab S, Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction., Mol Biol Evol, 12-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=29029241,, Application
      [Pubmed ID: 29029338], Molloy EK, Warnow T, To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods., Syst Biol, 03-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29029338,, Application
      [Pubmed ID: 29310567], Zheng Y, Janke A, Gene flow analysis method, the D-statistic, is robust in a wide parameter space., BMC Bioinformatics, 01-08-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29310567,, Application
      [Pubmed ID: 29462495], Luo A, Ling C, Ho SYW, Zhu CD, Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios., Syst Biol, 09-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29462495,, Application
      [Pubmed ID: 29495636], Sayyari E, Mirarab S, Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies., Genes (Basel), 02-28-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29495636,, Application
      [Pubmed ID: 29530498], Vachaspati P, Warnow T, SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space., Mol Phylogenet Evol, 07-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29530498,, Application
      [Pubmed ID: 29534152], Escalona M, Rocha S, Posada D, NGSphy: phylogenomic simulation of next-generation sequencing data., Bioinformatics, 07-15-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29534152,, Application
      [Pubmed ID: 29568323], Christensen S, Molloy EK, Vachaspati P, Warnow T, OCTAL: Optimal Completion of gene trees in polynomial time., Algorithms Mol Biol, 03-15-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29568323,, Application
      [Pubmed ID: 29710372], Knowles LL, Huang H, Sukumaran J, Smith SA, A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories., Am J Bot, 03-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29710372,, Application
      [Pubmed ID: 29745851], Vachaspati P, Warnow T, SIESTA: enhancing searches for optimal supertrees and species trees., BMC Genomics, 05-08-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29745851,, Application
      [Pubmed ID: 29745866], Zhang C, Rabiee M, Sayyari E, Mirarab S, ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees., BMC Bioinformatics, 05-08-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29745866,, Application
      [Pubmed ID: 29950018], Lafond M, Meghdari Miardan M, Sankoff D, Accurate prediction of orthologs in the presence of divergence after duplication., Bioinformatics, 07-01-2018, https://www.ncbi.nlm.nih.gov/pubmed/?term=29950018,, Application
      [Pubmed ID: 30393186], Rabiee M, Sayyari E, Mirarab S, Multi-allele species reconstruction using ASTRAL., Mol Phylogenet Evol, 01-01-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=30393186,, Application
      [Pubmed ID: 30825307], Schrempf D, Minh BQ, von Haeseler A, Kosiol C, Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity., Mol Biol Evol, 06-01-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=30825307,, Application
      [Pubmed ID: 30903171], Siu-Ting K, Torres-Sánchez M, San Mauro D, Wilcockson D, Wilkinson M, Pisani D, O'Connell MJ, Creevey CJ, Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics., Mol Biol Evol, 06-01-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=30903171,, Application
      [Pubmed ID: 31290974], Rabiee M, Mirarab S, INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores., Syst Biol, 03-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=31290974,, Application
      [Pubmed ID: 31360216], Molloy EK, Warnow T, Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge., Algorithms Mol Biol, 07-19-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=31360216,, Application
      [Pubmed ID: 31510668], Molloy EK, Warnow T, TreeMerge: a new method for improving the scalability of species tree estimation methods., Bioinformatics, 07-15-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=31510668,, Application
      [Pubmed ID: 31545363], Balaban M, Sarmashghi S, Mirarab S, APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments., Syst Biol, 05-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=31545363,, Application
      [Pubmed ID: 32299337], Rabiee M, Mirarab S, Forcing external constraints on tree inference using ASTRAL., BMC Genomics, 04-16-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32299337,, Application
      [Pubmed ID: 32502238], Morel B, Kozlov AM, Stamatakis A, Szöllősi GJ, GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene  Family Tree Inference under Gene Duplication, Transfer, and Loss., Mol Biol Evol, 09-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32502238,, Application
      [Pubmed ID: 32750133], Van Dam MH, Henderson JB, Esposito L, Trautwein M, Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction., Syst Biol, 02-10-2021, https://www.ncbi.nlm.nih.gov/pubmed/?term=32750133,, Application
      [Pubmed ID: 32886770], Zhang C, Scornavacca C, Molloy EK, Mirarab S, ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy., Mol Biol Evol, 11-01-2020, https://www.ncbi.nlm.nih.gov/pubmed/?term=32886770,, Application
      [Pubmed ID: 33616672], Shen XX, Steenwyk JL, Rokas A, Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data., Syst Biol, 02-22-2021, https://www.ncbi.nlm.nih.gov/pubmed/?term=33616672,, 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).