An official website of the United States government
GSR: Simulator - Simprot
| Attribute | Value |
|---|---|
| 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 | 18 years, 7 months ago |
| Homepage | http://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 evaluated | 05-16-2019 (1794 days ago) |
| 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Protein Sequence, |
| Variations | Multiallelic Marker, Amino acid variation, Insertion and Deletion, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| 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 | Codon and Amino Acid Models, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Graphical User Interface, Web-based, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | C or C++, |
| License | Other (Ncsa open source license), |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using Simprot has been provided.
Please propose new citations if you are aware of publications that use this software.