Literature DB >> 23709637

SLiM: simulating evolution with selection and linkage.

Philipp W Messer1.   

Abstract

SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure, various models for selection and dominance of new mutations, arbitrary gene structure, and user-defined recombination maps.

Keywords:  background selection; genetic hitchhiking; population genetic simulation

Mesh：

Year:  2013        PMID： 23709637      PMCID： PMC3730910          DOI： 10.1534/genetics.113.152181

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  13 in total

Review 1.  Computer simulations: tools for population and evolutionary genetics.

Authors:  Sean Hoban; Giorgio Bertorelle; Oscar E Gaggiotti
Journal:  Nat Rev Genet       Date:  2012-01-10       Impact factor: 53.242

2.  simuPOP: a forward-time population genetics simulation environment.

Authors:  Bo Peng; Marek Kimmel
Journal:  Bioinformatics       Date:  2005-07-14       Impact factor: 6.937

3.  A flexible forward simulator for populations subject to selection and demography.

Authors:  Ryan D Hernandez
Journal:  Bioinformatics       Date:  2008-10-07       Impact factor: 6.937

4.  Exploring population genetic models with recombination using efficient forward-time simulations.

Authors:  Badri Padhukasahasram; Paul Marjoram; Jeffrey D Wall; Carlos D Bustamante; Magnus Nordborg
Journal:  Genetics       Date:  2008-04       Impact factor: 4.562

5.  Simulation of genes and genomes forward in time.

Authors:  Antonio Carvajal-Rodríguez
Journal:  Curr Genomics       Date:  2010-03       Impact factor: 2.236

6.  A comparison of models to infer the distribution of fitness effects of new mutations.

Authors:  Athanasios Kousathanas; Peter D Keightley
Journal:  Genetics       Date:  2013-01-22       Impact factor: 4.562

7.  Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.

Authors:  Kirk E Lohmueller; Anders Albrechtsen; Yingrui Li; Su Yeon Kim; Thorfinn Korneliussen; Nicolas Vinckenbosch; Geng Tian; Emilia Huerta-Sanchez; Alison F Feder; Niels Grarup; Torben Jørgensen; Tao Jiang; Daniel R Witte; Annelli Sandbæk; Ines Hellmann; Torsten Lauritzen; Torben Hansen; Oluf Pedersen; Jun Wang; Rasmus Nielsen
Journal:  PLoS Genet       Date:  2011-10-13       Impact factor: 5.917

8.  Limits to the rate of adaptive substitution in sexual populations.

Authors:  Daniel B Weissman; Nicholas H Barton
Journal:  PLoS Genet       Date:  2012-06-07       Impact factor: 5.917

9.  Fregene: simulation of realistic sequence-level data in populations and ascertained samples.

Authors:  Marc Chadeau-Hyam; Clive J Hoggart; Paul F O'Reilly; John C Whittaker; Maria De Iorio; David J Balding
Journal:  BMC Bioinformatics       Date:  2008-09-08       Impact factor: 3.169

10.  Pervasive natural selection in the Drosophila genome?

Authors:  Guy Sella; Dmitri A Petrov; Molly Przeworski; Peter Andolfatto
Journal:  PLoS Genet       Date:  2009-06-05       Impact factor: 5.917
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  75 in total

1.  Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones.

Authors:  Fabrizio Mafessoni; Michael Lachmann
Journal:  Genetics       Date:  2015-10-23       Impact factor: 4.562

2.  The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses.

Authors:  Armando Caballero; Albert Tenesa; Peter D Keightley
Journal:  Genetics       Date:  2015-10-19       Impact factor: 4.562

3.  Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.

Authors:  Fernando Racimo
Journal:  Genetics       Date:  2015-11-23       Impact factor: 4.562

4.  Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.

Authors:  Benjamin C Haller; Jared Galloway; Jerome Kelleher; Philipp W Messer; Peter L Ralph
Journal:  Mol Ecol Resour       Date:  2019-02-21       Impact factor: 7.090

5.  Obstruction of adaptation in diploids by recessive, strongly deleterious alleles.

Authors:  Zoe June Assaf; Dmitri A Petrov; Jamie R Blundell
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-04       Impact factor: 11.205

6.  The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations.

Authors:  Ramesh Arunkumar; Rob W Ness; Stephen I Wright; Spencer C H Barrett
Journal:  Genetics       Date:  2014-12-30       Impact factor: 4.562

7.  Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences.

Authors:  Marty Kardos; Anna Qvarnström; Hans Ellegren
Journal:  Genetics       Date:  2017-01-18       Impact factor: 4.562

8.  Evidence that the rate of strong selective sweeps increases with population size in the great apes.

Authors:  Kiwoong Nam; Kasper Munch; Thomas Mailund; Alexander Nater; Maja Patricia Greminger; Michael Krützen; Tomàs Marquès-Bonet; Mikkel Heide Schierup
Journal:  Proc Natl Acad Sci U S A       Date:  2017-01-30       Impact factor: 11.205

9.  Evaluating Sequence-Based Genomic Prediction with an Efficient New Simulator.

Authors:  Miguel Pérez-Enciso; Natalia Forneris; Gustavo de Los Campos; Andrés Legarra
Journal:  Genetics       Date:  2016-12-02       Impact factor: 4.562

10.  The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

Authors:  Casper-Emil T Pedersen; Kirk E Lohmueller; Niels Grarup; Peter Bjerregaard; Torben Hansen; Hans R Siegismund; Ida Moltke; Anders Albrechtsen
Journal:  Genetics       Date:  2016-11-30       Impact factor: 4.562
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