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GSR: Simulator - CASS
| Attribute | Value |
|---|---|
| Title | CASS |
| Short Description | Protein Sequence Simulation |
| Long Description | CASS provides simulated protein (codon) sequences from a population genetic context with a protein structure-dependent explicit genotype-phenotype map. |
| Version | 1.1 |
| Project Started | 2011 |
| Last Release | 13 years, 5 months ago |
| Homepage | https://liberles.cst.temple.edu/Software/CASS/index.html |
| Citations | Grahnen JA and Liberles DA, CASS: Protein sequence simulation with explicit genotype-phenotype mapping, Trends in Evolutionary Biology, Trends in Evolutionary Biology, Nov. 13, 2012 |
| GSR Certification | ✔ Accessibility |
| Last evaluated | March 8, 2018 (3166 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Protein Sequence, |
| Variations | |
| Simulation Method | Forward-time, Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, Other, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, Other, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | Single-locus, Codon-based, Phenotypic Trait, |
| Models | Directional Selection, Epistasis, |
| Recombination | |
| Mutation Models | Codon and Amino Acid Models, Heterogeneity among Sites, |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 1
The following 1 publications are selected examples of applications that used CASS.
2011
Grahnen JA, Nandakumar P, Kubelka J, Liberles DA, Biophysical and structural considerations for protein sequence evolution., BMC Evol Biol, Dec. 16, 2011 [Abstract]