GSR: Simulator - CS-PSeq-Gen

Basic Package Attributes
AttributeValue
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 18 years, 8 months ago
Homepagehttp://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 ]
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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,
VariationsAmino acid variation,
Simulation MethodPhylogenetic,
Input
Data TypeAncestral Sequence,
File formatPhylip,
Output
Data TypeGenotype or Sequence, Individual Relationship,
Sequencing Reads
File FormatFasta 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 ModelsCodon and Amino Acid Models, Heterogeneity among Sites,
Events Allowed
Other
Interface
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
License
GSR Certification

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