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GSR: Simulator - CS-PSeq-Gen
The CS-PSeq-Gen package is not yet public.
| Attribute | Value |
|---|---|
| Title | CS-PSeq-Gen |
| Short Description | A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny |
| Long Description | CS-PSeq-Gen is a program derived from PSeq-Gen, a program developed by Nick C. Grassly and Andrew Rambaut, designed to simulate the evolution of protein sequences along evolutionary trees. CS-PSeq-Gen modifications are related to the aim of simulating the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny: the "root sequence" that initiates the simulation, or the rate heterogeneity among sites are specific on each particular protein family. CS-Pseq-Gen will allow simulations to take such information into account. As well, exploring the evolution of one protein family and testing hypotheses makes often it necessary to have some control on the variability of the parameters. CS-PSeq-Gen will allow some control on the simulated tree / branch lengths around an average value. Finally, a particular category of applications for such simulations is the search for the significant co-evolution of sites. CS-PSeq-Gen offers some facilities to generate sequences under such hypotheses, and propose a basic scheme for their detection, that can be easily adapted by programmers. |
| Version | 1.0 |
| Project Started | 2001 |
| Last Release | 22 years, 1 month ago |
| Homepage | http://bioserv.rpbs.univ-paris-diderot.fr/software/CS-PSeq-Gen/ |
| Citations | Tufféry P, CS-PSeq-Gen: simulating the evolution of protein sequence under constraints., Bioinformatics, 07-01-2002 [ 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. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Protein Sequence, |
| Variations | Amino acid variation, |
| Simulation Method | Phylogenetic, |
| Input | |
| Data Type | Ancestral Sequence, |
| File format | Phylip, |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, Phylip, |
| 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 | |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using CS-PSeq-Gen has been provided.
Please propose new citations if you are aware of publications that use this software.