simuPOP

Basic Package Attributes
Attribute	Value
Title	simuPOP
Short Description	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment.
Long Description	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease.
Version	1.1.7
Project Started	2005
Last Release	2 years, 10 months ago
Homepage	http://simupop.sourceforge.net/
Citations	Peng B, Amos CI, Forward-time simulations of non-random mating populations using simuPOP., Bioinformatics, June 1, 2008 [Abstract, cited in PMC ] Peng B, Kimmel M, simuPOP: a forward-time population genetics simulation environment., Bioinformatics, Sept. 15, 2005 [Abstract, cited in PMC ]
GSR Certification	✔Accessibility ✔Documentation ✔Application ✔Support
Last evaluated	Feb. 1, 2016 (1021 days ago)

Detailed Attributes
Attribute Category	Attribute
Target
Type of Simulated Data	Genotype at Genetic Markers, Diploid DNA Sequence, Haploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA,
Variations	Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite,
Simulation Method	Forward-time, Resample Existing Data,
Input
Data Type	Saved simulation, Other (Controlled by script),
File format	Fstat, Genepop, MS, Phylip,
Output
Data Type	Genotype or Sequence, Phenotypic Trait, Individual Relationship, Demographic, Mutation, Linkage Disequilibrium, Diversity Measures, Fitness,
Sequencing Reads	Other (Many stocked or self-defined statistics, including association tests and effective population size),
File Format	Fstat, Genepop, MS, Phylip, STRUCTURE, Program Specific (Self-defined binary format), Other (Recipes in cookbook),
Sample Type	Random or Independent, Sibpairs, Trios and Nuclear Families, Extended or Complete Pedigrees, Case-control, Longitudinal,
Phenotype
Trait Type	Binary or Qualitative, Quantitative, Multiple,
Determinants	Single Genetic Marker, Multiple Genetic Markers, Sex-linked, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction,
Evolutionary Features
Demographic
Population Size Changes	Constant Size, Exponential Growth or Decline, Bottleneck, Carrying Capacity, User Defined,
Gene Flow	Stepping Stone Models, Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population, User-defined Matrix,
Spatiality
Life Cycle	Discrete Generation Model, Age structured, Overlapping Generation,
Mating System	Random Mating, Monogamous, Polygamous, Haplodiploid, Selfing, Age- or Stage-Specific, Assortative or Disassortative, Other (Arbitrary nonrandom mating schemes could be defined),
Fecundity	Constant Number, Randomly Distributed, Individually Determined,
Natural Selection
Determinant	Single-locus, Multi-locus, Fitness of Offspring, Phenotypic Trait, Environmental Factors,
Models	Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Random Fitness Effects, Disruptive, Phenotype Threshold, Frequency-Dependent, Other (Many others),
Recombination	Uniform, Varying Recombination Rates, Gene Conversion Allowed,
Mutation Models	Two-allele Mutation Model, Markov DNA Evolution Models, k-Allele Model, Stepwise Mutation Model, Heterogeneity among Sites, Others (Many other mutation models such as context-sensitive models),
Events Allowed	Population Merge and Split, Varying Demographic Features, Population Events, Varying Genetic Features, Change of Mating Systems,
Other
Interface	Script-based (Python),
Development
Tested Platforms	Windows, Mac OS X, Linux and Unix, Solaris,
Language	C or C++, R, Python,
License	GNU Public License (V3),
GSR Certification	Accessibility, Documentation, Application, Support,

The following 62 publications are selected examples of applications that used simuPOP.

2016

Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MG, Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data., Mol Biol Evol, April 1, 2016 [Abstract]
Ogbunugafor CB, Wylie CS, Diakite I, Weinreich DM, Hartl DL, Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance., PLoS Comput Biol, Jan. 1, 2016 [Abstract]
Hackinger S, Kraaijenbrink T, Xue Y, Mezzavilla M, Asan, van Driem G, Jobling MA, de Knijff P, Tyler-Smith C, Ayub Q, Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas., Hum Genet, April 1, 2016 [Abstract]
Picq S, McMillan WO, Puebla O, Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)., Ecol Evol, April 1, 2016 [Abstract]
Risso DS, Mezzavilla M, Pagani L, Robino A, Morini G, Tofanelli S, Carrai M, Campa D, Barale R, Caradonna F, Gasparini P, et al., Global diversity in the TAS2R38 bitter taste receptor: revisiting a classic evolutionary PROPosal., Sci Rep, May 3, 2016 [Abstract]
Brousseau L, Postolache D, Lascoux M, Drouzas AD, Källman T, Leonarduzzi C, Liepelt S, Piotti A, Popescu F, Roschanski AM, Zhelev P, et al., Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe., PLoS One, Jan. 1, 2016 [Abstract]
Calboli FC, Byström P, Merilä J, A test for within-lake niche differentiation in the nine-spined sticklebacks (Pungitius pungitius)., Ecol Evol, July 1, 2016 [Abstract]
Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR, Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees., Evol Appl, Sept. 1, 2016 [Abstract]

2015

Mezzavilla M, Geppert M, Tyler-Smith C, Roewer L, Xue Y, Insights into the origin of rare haplogroup C3* Y chromosomes in South America from high-density autosomal SNP genotyping., Forensic Sci Int Genet, March 1, 2015 [Abstract]
Polley S, Louzada S, Forni D, Sironi M, Balaskas T, Hains DS, Yang F, Hollox EJ, Evolution of the rapidly mutating human salivary agglutinin gene (DMBT1) and population subsistence strategy., Proc Natl Acad Sci U S A, April 21, 2015 [Abstract]
Terhorst J, Schlötterer C, Song YS, Multi-locus analysis of genomic time series data from experimental evolution., PLoS Genet, April 1, 2015 [Abstract]
Ayub Q, Mezzavilla M, Pagani L, Haber M, Mohyuddin A, Khaliq S, Mehdi SQ, Tyler-Smith C, The Kalash genetic isolate: ancient divergence, drift, and selection., Am J Hum Genet, May 7, 2015 [Abstract]

2014

Yang P, Wu M, Guo J, Kwoh CK, Przytycka TM, Zheng J, LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms., BMC Bioinformatics, Feb. 17, 2014 [Abstract]
Song Y, Lan Z, Kohn MH, Mitochondrial DNA phylogeography of the norway rat., PLoS One, Jan. 1, 2014 [Abstract]
Waples RS, Antao T, Intermittent breeding and constraints on litter size: consequences for effective population size per generation (Ne ) and per reproductive cycle (Nb )., Evolution, June 1, 2014 [Abstract]
de Villemereuil P, Frichot É, Bazin É, François O, Gaggiotti OE, Genome scan methods against more complex models: when and how much should we trust them?, Mol Ecol, April 1, 2014 [Abstract]
Kamvar ZN, Tabima JF, Grünwald NJ, Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction., PeerJ, Jan. 1, 2014 [Abstract]
Waples RS, Antao T, Luikart G, Effects of Overlapping Generations on Linkage Disequilibrium Estimates of Effective Population Size., Genetics, April 8, 2014 [Abstract]
Veeramah KR, Gutenkunst RN, Woerner AE, Watkins JC, Hammer MF, Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans., Mol Biol Evol, Sept. 1, 2014 [Abstract]
Arnqvist G, Vellnow N, Rowe L, The effect of epistasis on sexually antagonistic genetic variation., Proc Biol Sci, July 22, 2014 [Abstract]
Duforet-Frebourg N, Bazin E, Blum MG, Genome scans for detecting footprints of local adaptation using a Bayesian factor model., Mol Biol Evol, Sept. 1, 2014 [Abstract]
Rasić G, Endersby NM, Williams C, Hoffmann AA, Using Wolbachia-based release for suppression of Aedes mosquitoes: insights from genetic data and population simulations., Ecol Appl, July 1, 2014 [Abstract]
Foll M, Gaggiotti OE, Daub JT, Vatsiou A, Excoffier L, Widespread signals of convergent adaptation to high altitude in Asia and america., Am J Hum Genet, Oct. 2, 2014 [Abstract]

2013

Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD, BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge, BMC Medical Genomics, May 7, 2013 [Abstract]
Roux C, Pauwels M, Ruggiero MV, Charlesworth D, Castric V, Vekemans X, Recent and ancient signature of balancing selection around the S-locus in Arabidopsis halleri and A. lyrata., Mol Biol Evol, Feb. 1, 2013 [Abstract]
Xu Y, Wu Y, Song C, Zhang H, Simulating realistic genomic data with rare variants., Genet Epidemiol, Feb. 1, 2013 [Abstract]
Fariello MI, Boitard S, Naya H, SanCristobal M, Servin B, Detecting signatures of selection through haplotype differentiation among hierarchically structured populations., Genetics, March 1, 2013 [Abstract]
Pritchard VL, Edmands S, The genomic trajectory of hybrid swarms: outcomes of repeated crosses between populations of Tigriopus californicus., Evolution, March 1, 2013 [Abstract]
Abdalla S, Al-Hadeethi Y, Genes alternations with exposure time of environmental factors., Gene, Oct. 10, 2013 [Abstract]
De Maio N, Schlötterer C, Kosiol C, Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models., Mol Biol Evol, Oct. 1, 2013 [Abstract]
Li B, Kimmel M, Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates., Genetics, Oct. 1, 2013 [Abstract]
Jiang PP, Corbett-Detig RB, Hartl DL, Lozovsky ER, Accessible mutational trajectories for the evolution of pyrimethamine resistance in the malaria parasite Plasmodium vivax., J Mol Evol, Sept. 1, 2013 [Abstract]
Hoban SM, Mezzavilla M, Gaggiotti OE, Benazzo A, van Oosterhout C, Bertorelle G, High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study., BMC Bioinformatics, Oct. 16, 2013 [Abstract]
Sim A, Tsagkrasoulis D, Montana G, Random forests on distance matrices for imaging genetics studies., Stat Appl Genet Mol Biol, Dec. 1, 2013 [Abstract]

2012

Pérez-Figueroa A, Wallen RL, Antao T, Coombs JA, Schwartz ML, White PJ, Luikart G, Conserving genomic variability in large mammals: Effect of population fluctuations and variance in male reproductive success on variability in Yellowstone bison, Biological Conservation, June 1, 2012 [Abstract]
Papetti C, Pujolar JM, Mezzavilla M, La Mesa M, Rock J, Zane L, Patarnell T, Population genetic structure and gene flow patterns between populations of the Antarctic icefish Chionodraco rastrospinosus, Journal of Biogeography, Feb. 6, 2012 [Abstract]
Wang Y, Gjuvsland AB, Vik JO, Smith NP, Hunter PJ, Omholt SW, Parameters in dynamic models of complex traits are containers of missing heritability., PLoS Comput Biol, Jan. 1, 2012 [Abstract]
Singhal S, Moritz C, Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard., Evolution, May 1, 2012 [Abstract]
Pinelli M, Scala G, Amato R, Cocozza S, Miele G, Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2., BMC Bioinformatics, June 14, 2012 [Abstract]
Boraska V, Jerončić A, Colonna V, Southam L, Nyholt DR, Rayner NW, Perry JR, Toniolo D, Albrecht E, Ang W, Bandinelli S, et al., Genome-wide meta-analysis of common variant differences between men and women., Hum Mol Genet, Nov. 1, 2012 [Abstract]
Cheung YH, Wang G, Leal SM, Wang S, A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders., Genet Epidemiol, Nov. 1, 2012 [Abstract]
Yoshizawa M, Ashida G, Jeffery WR, Parental genetic effects in a cavefish adaptive behavior explain disparity between nuclear and mitochondrial DNA., Evolution, Sept. 1, 2012 [Abstract]
Niederer SA, Land S, Omholt SW, Smith NP, Interpreting genetic effects through models of cardiac electromechanics., Am J Physiol Heart Circ Physiol, Dec. 1, 2012 [Abstract]
Vasemägi A, Nilsson J, McGinnity P, Cross T, O'Reilly P, Glebe B, Peng B, Berg PR, Primmer CR, Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon., Comp Funct Genomics, Jan. 1, 2012 [Abstract]

2011

Pujolar JM, Bevacqua D, Capoccioni F, Ciccotti E, De Leo GA, Zane L, No apparent genetic bottleneck in the demographically declining European eel using molecular genetics and forward-time simulations, Conservation Genetics, June 1, 2011 [Abstract]
Gleimer M, Wahl AR, Hickman HD, Abi-Rached L, Norman PJ, Guethlein LA, Hammond JA, Draghi M, Adams EJ, Juo S, Jalili R, et al., Although divergent in residues of the peptide binding site, conserved chimpanzee Patr-AL and polymorphic human HLA-A*02 have overlapping peptide-binding repertoires., J Immunol, Feb. 1, 2011 [Abstract]
Odong TL, van Heerwaarden J, Jansen J, van Hintum TJ, van Eeuwijk FA, Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?, Theor Appl Genet, July 1, 2011 [Abstract]
Bortolotto E, Bucklin A, Mezzavilla M, Zane L, Patarnello T, Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba., BMC Genet, April 12, 2011 [Abstract]
Arnqvist G, Assortative mating by fitness and sexually antagonistic genetic variation., Evolution, July 1, 2011 [Abstract]
Palin K, Campbell H, Wright AF, Wilson JF, Durbin R, Identity-by-descent-based phasing and imputation in founder populations using graphical models., Genet Epidemiol, Dec. 1, 2011 [Abstract]
Swartz MD, Peng B, Reyes-Gibby C, Shete S, Using Ascertainment for Targeted Resequencing to Increase Power to Identify Causal Variants., Stat Interface, Jan. 1, 2011 [Abstract]

2010

Antao T, Pérez-Figueroa A, Luikart G, Early detection of population declines: high power of genetic monitoring using effective population size estimators, Evolutionary Applications, Aug. 3, 2010 [Abstract]
Peng B, Amos CI, Forward-time simulation of realistic samples for genome-wide association studies., BMC Bioinformatics, Sept. 1, 2010 [Abstract]
Zheng J, Khil PP, Camerini-Otero RD, Przytycka TM, Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome., Genome Biol, Jan. 1, 2010 [Abstract]
Peng B, Liu X, Simulating sequences of the human genome with rare variants., Hum Hered, Jan. 1, 2010 [Abstract]

2009

Gu X, Frankowski RF, Rosner GL, Relling M, Peng B, Amos CI, A modified forward multiple regression in high-density genome-wide association studies for complex traits., Genet Epidemiol, Sept. 1, 2009 [Abstract]
Wu CC, Shete S, Chen WV, Peng B, Lee AT, Ma J, Gregersen PK, Amos CI, Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis., Hum Genet, Aug. 1, 2009 [Abstract]
Gendzekhadze K, Norman PJ, Abi-Rached L, Graef T, Moesta AK, Layrisse Z, Parham P, Co-evolution of KIR2DL3 with HLA-C in a human population retaining minimal essential diversity of KIR and HLA class I ligands., Proc Natl Acad Sci U S A, Nov. 3, 2009 [Abstract]

2008

Stacey A, Sheffield NC, Crandall KA, Calculating expected DNA remnants from ancient founding events in human population genetics., BMC Genet, Oct. 17, 2008 [Abstract]

2007

Peng B, Kimmel M, Simulations provide support for the common disease-common variant hypothesis., Genetics, Feb. 1, 2007 [Abstract]
Peng B, Amos CI, Kimmel M, Forward-time simulations of human populations with complex diseases., PLoS Genet, March 23, 2007 [Abstract]
Norman PJ, Abi-Rached L, Gendzekhadze K, Korbel D, Gleimer M, Rowley D, Bruno D, Carrington CV, Chandanayingyong D, Chang YH, Crespí C, et al., Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans., Nat Genet, Sept. 1, 2007 [Abstract]

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