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GeneClass specifications

Information


Unique identifier OMICS_15310
Name GeneClass
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A data file containing a mixture of diploid or haploid data, the level of ploidy, the reference dataset.
Output data The criterion -log10(L) or the genetic distance for the distance-based method, the probabilities, the number of alleles and genes per population and locus, allelic frequencies, heterozygotes proportions, and Nei’s gene diversity.
Output format CSV
Operating system Unix/Linux, Windows
Computer skills Medium
Version 2.0
Stability Stable
Source code URL http://www1.montpellier.inra.fr/CBGP/software/GeneClass/GeneClass2/GeneClass2.tar.gz
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Sylvain Piry

Publication for GeneClass

GeneClass citations

 (250)
library_books

Weak population structure and no genetic erosion in Pilosocereus aureispinus: A microendemic and threatened cactus species from eastern Brazil

2018
PLoS One
PMCID: 5890996
PMID: 29630653
DOI: 10.1371/journal.pone.0195475

[…] previous results of our population structure analyses, we conclude that BARRIER has identified a subtle, more sensible restriction to gene flow among populations. Further the analysis implemented in GENECLASS2 detected four possible migrants in 91 individuals (), indicating that seed and/or pollen movement among all the localities may eventually occur. Although very little is known about the repr […]

call_split

Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa

2018
PLoS One
PMCID: 5882123
PMID: 29614097
DOI: 10.1371/journal.pone.0194189
call_split See protocol

[…] o detect first-generation migrants (i.e., the individuals with a high probability of being born at one sampling locality), we divided the GB165 dataset in GB_Cantanhez, GB_Cufada, and GB_Boé and used GENECLASS version 2.0 [] to estimate two likelihood-based tests statistics: Lh (more adequate when the source population might not have been sampled) and Lh/Lmax (better when all source populations we […]

call_split

Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape

2018
PLoS One
PMCID: 5862458
PMID: 29561865
DOI: 10.1371/journal.pone.0193495
call_split See protocol

[…] rived from bootstrapping) did not intercept the axis of r = 0[].To examine whether the individuals were born in the location from which they were sampled, assignment/exclusion tests were performed in GENECLASS, version 2.0 []. The Bayesian approach with re-sampling algorithm [] was used with 10,000 individuals at an assignment threshold (alpha, α) value of 0.01. The likelihood ratio test statistic […]

call_split

Genetic and oceanographic tools reveal high population connectivity and diversity in the endangered pen shell Pinna nobilis

2018
Sci Rep
PMCID: 5859023
PMID: 29555926
DOI: 10.1038/s41598-018-23004-2
call_split See protocol

[…] ations and a run-length of 500,000 iterations. The most likely K (number of groups) was inferred using the DeltaK criterion with STRUCTURE HARVESTER.Juveniles were assigned to adult populations using GENECLASS v. 2.0 under the Bayesian assignment method. Adult genotypes of each of the six sites were used as reference populations and juveniles (obtained solely in Mallorca and Banyuls) were then eit […]

call_split

Post epizootic salamander persistence in a disease free refugium suggests poor dispersal ability of Batrachochytrium salamandrivorans

2018
Sci Rep
PMCID: 5830533
PMID: 29491409
DOI: 10.1038/s41598-018-22225-9
call_split See protocol

[…] al. as well as the posterior likelihood of the data as described by Pritchard et al., only when both methods identified the same K, we inferred this K as the most likely. Lastly, we used the program GENECLASS2 in order to assign individuals to their respective subpopulation (Bunderbos and Broek, e.g. Valbuena-Ureña et al.). […]

call_split

Single nucleotide polymorphisms in native South American Atlantic coast populations of smooth shelled mussels: hybridization with invasive European Mytilus galloprovincialis

2018
PMCID: 5824471
PMID: 29471805
DOI: 10.1186/s12711-018-0376-z
call_split See protocol

[…] iduals to population of origin was obtained by using the frequency criteria on the basis of multilocus genotype data [] in a self-assignment test with the leave-one-out (LOO) procedure implemented in GeneClass2.0 []. Individuals were considered to be correctly assigned to their location of origin if the assignment probability to that group was higher than any other assignment probability to any ot […]

Citations

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GeneClass institution(s)
Centre de Biologie et de Gestion des Populations, INRA, Campus International de Baillarguet, Monferrier-sur-Lez, France; Wildlife Genetics International, Nelson, Canada; CIRAD, Département Cultures Pérennes, Montpellier, France
GeneClass funding source(s)
This work was supported by grants from the CIRAD/INRA on ‘‘Approches biomathématiques et biotechnologiques pour l’identification génétique et la gestion adaptée des populations animales et végétales’’ and from the INRA SPE department on methods associated with realtime population genetics.

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