GSR: Simulator - Simprot

Basic Package Attributes
AttributeValue
Title Simprot
Short Description A program to simulate protein evolution by substitution, insertion and deletion
Long Description Protein evolution has been largely modelled by considering the amino acid substitution process; however they have been few studies of the process of insertion and deletion. Simprot allows for several models of amino acid substitution (PAM, JTT and PMB), allows for gamma distributed sites rates according to Yang's model, and implements a parameterised Qian and Goldstein distribution model for insertion and deletion.
Version 1.03
Project Started 2005
Last Release 15 years ago
Homepagehttp://www.uhnresearch.ca/labs/tillier/software.htm#3
Citations Pang A, Smith AD, Nuin PA, Tillier ER, SIMPROT: using an empirically determined indel distribution in simulations of protein evolution., BMC Bioinformatics, 09-27-2005 [ Abstract, cited in PMC ]
GSR Certification This package has been evaluated. No certificates were awarded at this time.
Last evaluated05-16-2019 (520 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 DataProtein Sequence,
VariationsMultiallelic Marker, Amino acid variation, Insertion and Deletion,
Simulation MethodPhylogenetic,
Input
Data TypeAncestral Sequence,
File format
Output
Data TypeGenotype or Sequence,
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 ModelsCodon and Amino Acid Models, Heterogeneity among Sites,
Events Allowed
Other
InterfaceGraphical User Interface, Web-based,
Development
Tested PlatformsWindows, Linux and Unix,
LanguageC or C++,
LicenseOther (Ncsa open source license),
GSR Certification

No example publication using Simprot has been provided.

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