GSR: Simulator - indel-Seq-Gen

Basic Package Attributes
AttributeValue
Title indel-Seq-Gen
Short Description A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies
Long Description indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the "true" multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods.
Version 2.1.03
Project Started 2010
Last Release 9 years, 10 months ago
Homepagehttp://bioinfolab.unl.edu/~cstrope/iSG/
Citations Strope CL, Scott SD, Moriyama EN, indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels., Mol Biol Evol, 03-01-2007 [ Abstract, cited in PMC ]
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Last evaluated10-15-2020 (2 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence, Protein Sequence,
VariationsAmino acid variation, Insertion and Deletion,
Simulation MethodPhylogenetic,
Input
Data TypeAncestral Sequence,
File format
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatFasta or Fastq,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation ModelsMarkov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites,
Events Allowed
Other
InterfaceCommand-line, Graphical User Interface (Through suitemsa (http://bioinfolab.unl.edu/~canderson/suitemsa/) ),
Development
Tested PlatformsWindows (Mingw), Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation,

No example publication using indel-Seq-Gen has been provided.

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