GSR: Simulator - CASS

Basic Package Attributes
AttributeValue
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 7 years, 5 months ago
Homepagehttps://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, 11-13-2012
GSR Certification

Accessibility
Documentation
Application
Support

Last evaluated03-08-2018 (954 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataProtein Sequence,
Variations
Simulation MethodForward-time, Phylogenetic,
Input
Data TypeAncestral Sequence, Other,
File formatOther,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatFasta 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
DeterminantSingle-locus, Codon-based, Phenotypic Trait,
ModelsDirectional Selection, Epistasis,
Recombination
Mutation ModelsCodon and Amino Acid Models, Heterogeneity among Sites,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsLinux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Support,

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, 12-16-2011 [Abstract]


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