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Protocols

GP specifications

Information


Unique identifier OMICS_12950
Name GP
Alternative name GenomePop
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.7.4
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Antonio Carvajal-Rodríguez

Publication for GenomePop

GP citations

 (9)
call_split

An Eigenvalue test for spatial principal component analysis

2017
BMC Bioinformatics
PMCID: 5732370
PMID: 29246102
DOI: 10.1186/s12859-017-1988-y
call_split See protocol

[…] To assess the performance of our test, we simulated genetic data under three migration models: island (IS) and stepping stone (SS), using the software GenomePop 2.7 [], and isolation by distance (IBD), using IBDSimV2.0 []. We simulated the IS and SS models with 4 populations, each with 25 individuals, and a single population under IBD with 100 indiv […]

call_split

Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow

2015
Curr Genomics
PMCID: 4460224
PMID: 26069460
DOI: 10.2174/1389202916666150313230943
call_split See protocol

[…] To test the ability of the Svd and SvdM methods for detecting the footprint of selection, the program GenomePop [] was used to simulate two populations of facultative hermaphrodites under divergent selection and migration. Each individual consisted of a diploid chromosome of length 1Mb of biallelic lo […]

library_books

Boosting forward time population genetic simulators through genotype compression

2013
BMC Bioinformatics
PMCID: 3700844
PMID: 23763838
DOI: 10.1186/1471-2105-14-192

[…] egulatory pathways, and epigenetic mechanisms, are studied using forward time simulators [,]. Although current simulators exist for efficiently simulating large genomic regions — FREGENE, SimuPOP, or GenomePop — the memory management techniques do not extend to arbitrary genotype representations like pathways or metabolic networks or other mutation types like insertions or rearrangements [,]. For […]

library_books

Computer Programs and Methodologies for the Simulation of DNA Sequence Data with Recombination

2013
Front Genet
PMCID: 3561691
PMID: 23378848
DOI: 10.3389/fgene.2013.00009

[…] r program does not force recombination breakpoints to occur between codons, thus allowing more realistic simulations (see Arenas and Posada, ). Concerning the forward-time approach, only the programs GenomePop (Carvajal-Rodriguez, ) and SFS_CODE (Hernandez, ) implement the simulation of coding sequences with recombination.Evolutionary scenarios that are not implemented in these programs can be sim […]

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

[…] brary of python functions that are required by the user to be “glued together” within a python script, which again has various different mating schemes and migration models at the users disposal [,]. GenomePop [] is an IBM that utilizes Markovian nucleotide or codon models of DNA mutation, such as the Jukes-Cantor or general time reversible mutation model to generate synonymous and non-synonymous […]

call_split

Fine scale detection of population specific linkage disequilibrium using haplotype entropy in the human genome

2010
BMC Genet
PMCID: 2873552
PMID: 20416085
DOI: 10.1186/1471-2156-11-27
call_split See protocol

[…] tion, shaping a continuous gradient from one end (r = 1) to the other end (r = 2.1E-9). For each locus, initial allele frequency k and 1 - k (0 ≤ k ≤ 1) for two alleles were randomly given. Using the GenomePop software [], the evolutionary process was simulated for 5,000 generations with the parameter of population size as 10,000 and mutation rate per locus as 2.0E-9. Then, 120 chromosomes for 60 […]


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GP institution(s)
Departamento de Bioquímica, Genética e Inmunología Universidad de Vigo, Vigo, Spain
GP funding source(s)
Grant CPE03-004-C2, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA); Dirección Xeral de Investigación e Desenvolvemento, Xunta de Galicia; Isidro Parga Pondal research fellowship, Xunta de Galicia (Spain)

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