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Citations per year

Number of citations per year for the bioinformatics software tool CoaSim
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Protocols

CoaSim specifications

Information


Unique identifier OMICS_06839
Name CoaSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained No

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Publication for CoaSim

CoaSim citations

 (6)
library_books

cophesim: a comprehensive phenotype simulator for testing novel association methods

2017
F1000Res
PMCID: 5605948
PMID: 28979766
DOI: 10.5256/f1000research.12938.r24718

[…] ental data, which may not be easily obtainable. One solution is to use artificial data simulated with specific assumptions.The best existing phenotype simulators, such as: GENOME , Plink , phenosim , CoaSim , Fregene , ForSim , QuantiNemo , GCTA , HapGen , SeqSimla , and SimRare offer qualitative and dichotomous simulated phenotype. But the known phenotype simulation software tools have some limi […]

library_books

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

2014
BMC Bioinformatics
PMCID: 3890628
PMID: 24387001
DOI: 10.1186/1471-2105-15-3

[…] tterns delineated by recombination hotspots along chromosomes in fine-mapping locations of disease loci. Over the past decade, a plethora of coalescent simulators have been developed, e.g. SelSim [], CoaSim [], FastCoal [], Mlcoalsim [], and RECOAL [], to name a few. Of them, five most representative and widely used coalescent simulators, Hudson’s ms [], msHOT [], Markovian Coalescent Simulator (M […]

call_split

A New Isolation with Migration Model along Complete Genomes Infers Very Different Divergence Processes among Closely Related Great Ape Species

2012
PLoS Genet
PMCID: 3527290
PMID: 23284294
DOI: 10.1371/journal.pgen.1003125
call_split See protocol

[…] For our simulation experiments, we simulated ancestral recombination graphs from the coalescent with recombination process using the CoaSim tool . From this we extracted local (tree) genealogies and simulated sequences over these using the Bio++ suite with the Jukes-Cantor JC69 substitution model. […]

library_books

A survey of genetic simulation software for population and epidemiological studies

2008
Hum Genomics
PMCID: 3525177
PMID: 19129092
DOI: 10.1186/1479-7364-3-1-79

[…] l step to unascertained simulated data. Currently, however, there are no easy ways of doing this, as additional user coding would be needed to adapt the sampling algorithms available in, for example, CoaSim,[]SimuPOP[-] or FREGENE[]. Furthermore, there are as yet no completely flexible ascertainment options that would allow, for example, simulation of cases from models with more than one partially […]

library_books

Simulation of Genomes: A Review

2008
Curr Genomics
PMCID: 2679650
PMID: 19440512
DOI: 10.2174/138920208784340759

[…] ining effect of selection and recombination and the Fearnhead set of programs [] allows the study of the impact of strong selection onto patterns of variability under different scenarios. Noteworthy, coasim [], cosi [], msHOT [], mlcoalsim [] and GENOME [] programs allow for a flexible and complete set of situations including recombination hotspots. Finally, the efficiency of the programs is very […]

library_books

The age and evolution of an antiviral resistance mutation in Drosophila melanogaster

2007
PMCID: 1914336
PMID: 17550883
DOI: 10.1098/rspb.2007.0611

[…] artial selective sweep of this haplotype has occurred, we tested whether there is less variation among the resistant haplotypes than expected by chance.We used coalescent simulations (performed using CoaSim ()) to assess the probability that genetic diversity within the resistant haplotype conformed to the expectation under a neutral coalescent. […]


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CoaSim institution(s)
Bioinformatics Research Center, University of Aarhus, Arhus, Denmark

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