IBDsim statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IBDsim
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Tool usage distribution map

This map represents all the scientific publications referring to IBDsim per scientific context
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Associated diseases

This word cloud represents IBDsim usage per disease context
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Popular tool citations

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Protocols

IBDsim specifications

Information


Unique identifier OMICS_15322
Name IBDsim
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License CeCILL version 2.1
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://www1.montpellier.inra.fr/CBGP/software/ibdsim/ressources/ibdsim/IBDSimV2.0_Sources.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Raphael Leblois

Publication for IBDsim

IBDsim citations

 (7)
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Artificial barriers prevent genetic recovery of small isolated populations of a low mobility freshwater fish

2018
Heredity
PMCID: 5943333
PMID: 29326479
DOI: 10.1038/s41437-017-0008-3
call_split See protocol

[…] le, Blois et al. ), we ran simulations using a generation-by-generation coalescent algorithm that can simulate spatially limited dispersal (and resulting background genetic structure), implemented in IBDsim 2.0 (Leblois et al. , ). Consistent with our G. marmoratus data set for each stream, simulated data sets had 90 diploid individuals genotyped at 8 independent microsatellite loci. Mutations of […]

library_books

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes

2017
Nat Commun
PMCID: 5566399
PMID: 28827725
DOI: 10.1038/s41467-017-00323-y

[…] e to restrict ourselves to analyzing regions that could only arise from a very small number of recent generations, up to and including those from third cousins. To examine this, we used the R-package IBDsim (see section on the predicted number of meioses from observed autozygous tract lengths) to simulate IBD sections in individuals separated by varying numbers of meioses. We then observed the lon […]

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Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta Analysis

2016
PLoS One
PMCID: 4873183
PMID: 27195493
DOI: 10.1371/journal.pone.0150991
call_split See protocol

[…] Next, we simulated genetic differentiation under a range of dispersal scenarios and compared these results with our microsatellite data. To do this, we used IBDSim v.2 [] to simulate genotypic data for multiple unlinked loci under a general isolation-by-distance model. IBDSim is based on a backward-in-time coalescent method that enables the generation of […]

library_books

Data Simulation in Machine Olfaction with the R Package Chemosensors

2014
PLoS One
PMCID: 3935855
PMID: 24586410
DOI: 10.1371/journal.pone.0088839

[…] framework for the distribution of data sets and software for data generation. Published packages for data simulation include the fwsim package for functional magnetic resonance imaging , the packages IBDsim and hapsim in statistical genetics , and the simFrame package for building a general-purpose framework for statistical simulations .Our manuscript is organized as follows. We begin with a desc […]

library_books

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations

2013
PMCID: 4844292
PMID: 27137364
DOI: 10.3390/plants2010016

[…] number of software tools using IBMs have been developed. These include EasyPop, a population genetics simulator to simulate neutral loci datasets under various mating schemes and migration models []; IBDSim, a program for simulating isolation by distance between individuals []; QuantiNemo, an individual-based model for simulating quantitative traits amongst individuals within heterogeneous “patche […]

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Clonality Despite Sex: The Evolution of Host Associated Sexual Neighborhoods in the Pathogenic Fungus Penicillium marneffei

2012
PLoS Pathog
PMCID: 3464222
PMID: 23055919
DOI: 10.1371/journal.ppat.1002851
call_split See protocol

[…] CA and DAPC analyses . To compare our inferred results against a model of a single continuous population structured by a dingle dispersal kernel and mutation rate we used the coalescent based program IBDsim . Additional distribution data for bamboo rats were collected from specimen databases AMNH, FMNH, NMNH, and the GBIF. We used the bioclim layers 1–21 at 30 sec from the world clim database in M […]


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IBDsim institution(s)
Muséum National d’Histoire Naturelle, UMR 5202 CNRS/MNHN ‘Origine, Structure et Evolution de la Biodiversité’, Paris, France; INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez, France; Université Montpellier 2, CNRS, Institut des sciences de l’Évolution, Montpellier, France

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