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GSR: Simulator - EggLib
| Attribute | Value |
|---|---|
| Title | EggLib |
| Short Description | EggLib is a C++/Python library and program package for evolutionary genetics and genomics. |
| Long Description | EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, coalescent simulations and Approximate Bayesian Computation. EggLib is a flexible Python module with a performant underlying C++ library (which can be used independently), and allows fast and intuitive development of Python programs and scripts. A number of pre-programmed applications of EggLib possibilities are available interactively. |
| Version | 2.1.4 |
| Project Started | 2012 |
| Last Release | 13 years, 1 month ago |
| Homepage | http://egglib.sourceforge.net/ |
| Citations | De Mita S, Siol M, EggLib: processing, analysis and simulation tools for population genetics and genomics., BMC Genet, April 11, 2012 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | Feb. 8, 2018 (2775 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, |
| Variations | Biallelic Marker (Neutral alleles), Multiallelic Marker (Neutral alleles), Single Nucleotide Variation (Neutral alleles), Microsatellite (Neutral alleles), |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, Individual Relationship (Phylogenetic trees), Linkage Disequilibrium (Using the library), Diversity Measures, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, MS, Program Specific (Ms format adapted for microsatellite data), |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Bottleneck, User Defined (User-defined population size change at any step), |
| Gene Flow | Stepping Stone Models, Island Models, Continent-Island Models, Admixed Population, User-defined Matrix, |
| Spatiality | |
| Life Cycle | |
| Mating System | Random Mating, Selfing, |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | Uniform, |
| Mutation Models | Two-allele Mutation Model, Markov DNA Evolution Models, k-Allele Model, Infinite-allele Model, Infinite-sites Model, Stepwise Mutation Model, |
| Events Allowed | Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, |
| Other | |
| Interface | Command-line, Script-based, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used EggLib.
2023
Youngblom MA, Shockey AC, Callaghan MM, Dillard JP, Pepperell CS, The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae., Microb Genom, May 1, 2023 [Abstract]
2022
Dubin CA, Voorhies M, Sil A, Teixeira MM, Barker BM, Brem RB, Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii., J Fungi (Basel), Nov. 22, 2022 [Abstract]