CS-PSeq-Gen

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Basic Package Attributes
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	16 years, 12 months 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, July 1, 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.

Detailed Attributes
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

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