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 | 11 years, 6 months 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, 04-11-2012 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 02-08-2018 (2234 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, 05-01-2023 [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), 11-22-2022 [Abstract]