Literature DB >> 16882649

Nemo: an evolutionary and population genetics programming framework.

Frédéric Guillaume1, Jacques Rougemont.   

Abstract

UNLABELLED: Nemo is an individual-based, genetically explicit and stochastic population computer program for the simulation of population genetics and life-history trait evolution in a metapopulation context. It comes as both a C++ programming framework and an executable program file. Its object-oriented programming design gives it the flexibility and extensibility needed to implement a large variety of forward-time evolutionary models. It provides developers with abstract models allowing them to implement their own life-history traits and life-cycle events. Nemo offers a large panel of population models, from the Island model to lattice models with demographic or environmental stochasticity and a variety of already implemented traits (deleterious mutations, neutral markers and more), life-cycle events (mating, dispersal, aging, selection, etc.) and output operators for saving data and statistics. It runs on all major computer platforms including parallel computing environments. AVAILABILITY: The source code, binaries and documentation are available under the GNU General Public License at http://nemo2.sourceforge.net.

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Mesh:

Year:  2006        PMID: 16882649     DOI: 10.1093/bioinformatics/btl415

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  49 in total

Review 1.  An overview of population genetic data simulation.

Authors:  Xiguo Yuan; David J Miller; Junying Zhang; David Herrington; Yue Wang
Journal:  J Comput Biol       Date:  2011-12-09       Impact factor: 1.479

2.  TreesimJ: a flexible, forward time population genetic simulator.

Authors:  Brendan O'Fallon
Journal:  Bioinformatics       Date:  2010-07-29       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.  Testing for spatially divergent selection: comparing QST to FST.

Authors:  Michael C Whitlock; Frederic Guillaume
Journal:  Genetics       Date:  2009-08-17       Impact factor: 4.562

6.  The role of phenotypic plasticity on population differentiation.

Authors:  M Schmid; F Guillaume
Journal:  Heredity (Edinb)       Date:  2017-07-26       Impact factor: 3.821

7.  skelesim: an extensible, general framework for population genetic simulation in R.

Authors:  Christian M Parobek; Frederick I Archer; Michelle E DePrenger-Levin; Sean M Hoban; Libby Liggins; Allan E Strand
Journal:  Mol Ecol Resour       Date:  2016-11-16       Impact factor: 7.090

8.  The G-matrix Simulator Family: Software for Research and Teaching.

Authors:  Adam G Jones; Reinhard Bürger; Stevan J Arnold
Journal:  J Hered       Date:  2018-10-31       Impact factor: 2.645

9.  Gene functional trade-offs and the evolution of pleiotropy.

Authors:  Frédéric Guillaume; Sarah P Otto
Journal:  Genetics       Date:  2012-09-14       Impact factor: 4.562

10.  Simulation of genes and genomes forward in time.

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

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