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Citations per year

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FlexQTL specifications


Unique identifier OMICS_18988
Name FlexQTL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.99
Stability Stable
Maintained Yes




No version available


  • person_outline Maria José Aranzana

Publication for FlexQTL

FlexQTL citations


Tools for Genetic Studies in Experimental Populations of Polyploids

Front Plant Sci
PMCID: 5915555
PMID: 29720992
DOI: 10.3389/fpls.2018.00513

[…] we also anticipate that more powerful QTL analyses can be performed by combining information over multiple populations. Approaches such as pedigree-informed analyses, implemented for diploids in the FlexQTL software (), could overcome some of the limitations imposed by the restrictions on population types in software for polyploids. However, it may take some time before such tools become translat […]


Genotyping by sequencing application on diploid rose and a resulting high density SNP based consensus map

PMCID: 5878828
PMID: 29619228
DOI: 10.1038/s41438-018-0021-6

[…] ose gaps may be caused by the lack of markers covering heterochromatic pericentromeric regions. This consensus map will serve as one of the basic components required in a pedigree-based QTL analysis (FlexQTL™) to facilitate marker–trait association studies. […]


An integrated approach for increasing breeding efficiency in apple and peach in Europe

PMCID: 5830435
PMID: 29507735
DOI: 10.1038/s41438-018-0016-3

[…] rkers. The format of its input files are compatible with output files from GenomeStudio (Illumina Inc., San Diego, CA, USA; http://www.illumina.com).FruitBreedomics successfully extended the software FlexQTL for use on SNP markers. FlexQTL was developed in the previous EU-HiDRAS project to enable multi-family analyses and was ready for the use of SSR markers. As thousands SNP markers can now be te […]


Clarifying sub genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree based QTL analysis

PMCID: 5676184
PMID: 29138689
DOI: 10.1038/hortres.2017.62

[…] ssociated with the SSC QTL, was also found flanking the current SSC QTL (van de Weg E, unpublished data). The SSR marker EMFv006 alleles were not able to differentiate between QTL alleles assigned by FlexQTL and was rendered not suitable for MAB applications. To determine if unknown polymorphism existed within the SSR marker EMFv006, analysis by high-resolution melting and amplicon sequencing was […]


Predicting Flowering Behavior and Exploring Its Genetic Determinism in an Apple Multi family Population Based on Statistical Indices and Simplified Phenotyping

Front Plant Sci
PMCID: 5461300
PMID: 28638387
DOI: 10.3389/fpls.2017.00858

[…] wn), and the similar small size of both genetic maps. Then sets of single SNPs were integrated into haploblocks, corresponding to successive 1 cM segments. Haplotypes were composed using the software FlexQTL™ (www.flexqtl.nl) and PediHaplotyper (Voorrips et al., ).Indices used in QTL analysis were BBI_res_norm_ax, γax, BBI_res_norm_pred, γpred, Ent¯g, Ent¯glmm,g, the BLUPs for genotypes × memory i […]


Genome enabled predictions for fruit weight and quality from repeated records in European peach progenies

BMC Genomics
PMCID: 5460546
PMID: 28583089
DOI: 10.1186/s12864-017-3781-8

[…] llow for the effect of permanent environment to be estimated. GBLUP was used for genomic predictions (and estimation of heritability and repeatability), instead of a weighted sum of QTL effects as in FlexQTL®;[]. Additionally, we implemented a repetition protocol to ensure numerical stability in spite of the stochastic variability embedded in cross-validation and Gibbs samplings (BGLR). Finally, t […]

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FlexQTL institution(s)
IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain; Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all’Adige, TN, Italy; Hendrix Genetics Research, Technology & Services B.V., Boxmeer, Netherlands; Plant Breeding, Wageningen University and Research Droevendaalsesteeg 1, Wageningen, Netherlands; IRTA, FruitCentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Lleida, Spain; PTP Science Park, Lodi, Italy; Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy; Consiglio per la Ricerca in Agricoltura e L’analisi Dell’economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, Roma, Italy; BFP, INRA, Villenave d’Ornon, France; GAFL, INRA, Montfavet, France; Università degli Studi di Milano, DiSAA, Milan, Italy; IRHS, INRA, SFR 4207 QuaSaV, Beaucouze, France
FlexQTL funding source(s)
Supported by the EU seventh Framework Programme by the FruitBreedomics project Nu. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops; IRTA-CRAG group received financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533)” and through the project AGL2015-68329-R, and from the CERCA Programme/Generalitat de Catalunya.

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