indel-Seq-Gen

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Basic Package Attributes
Attribute	Value
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, 6 months ago
Homepage	http://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, March 1, 2007 [Abstract, cited in PMC ]
GSR Certification	This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification .
Author verification	The 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 Category	Attribute
Target
Type of Simulated Data	Haploid DNA Sequence, Protein Sequence,
Variations	Amino acid variation, Insertion and Deletion,
Simulation Method	Phylogenetic,
Input
Data Type	Ancestral Sequence,
File format
Output
Data Type	Genotype or Sequence, Individual Relationship,
Sequencing Reads
File Format	Fasta 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 Models	Markov DNA Evolution Models, Codon and Amino Acid Models, Indels and Others, Heterogeneity among Sites,
Events Allowed
Other
Interface	Command-line, Graphical User Interface (Through suitemsa (http://bioinfolab.unl.edu/~canderson/suitemsa/) ),
Development
Tested Platforms	Windows (Mingw), Mac OS X, Linux and Unix,
Language	C or C++,
License	GNU Public License,
GSR Certification

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