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SPAGeDi specifications


Unique identifier OMICS_22330
Name SPAGeDi
Alternative name Spatial Pattern Analysis of Genetic Diversity
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Version 1.5
Stability Stable
Maintained Yes




No version available



  • person_outline Olivier J. Hardy

Publication for Spatial Pattern Analysis of Genetic Diversity

SPAGeDi citations


Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi Locus Genome Wide Association Studies

Front Plant Sci
PMCID: 5933171
PMID: 29755499
DOI: 10.3389/fpls.2018.00561

[…] ; Tables –). However, only one and six significantly associated SNPs were detected when using MLM (R package GAPIT) and FarmCPU (R package FarmCPU; PCA+K, where PCA and K were calculated by GAPIT and SpAGeDi, respectively) models, respectively (P = 0.05/43427 = 1.15 × 10−6; Table ). This suggested that these multi-locus methods were more powerful when used for detecting the QTNs for regeneration-r […]


Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits

PLoS One
PMCID: 5884518
PMID: 29617461
DOI: 10.1371/journal.pone.0194670
call_split See protocol

[…] entity matrix, a~N(0, 2Gσa2)–the vector of random individual plant genetic effects, with σa2—within population (additive genetic) variance and G–Loisselle’s kinship coefficient [] matrix estimated in SPAGeDi 1.5 [] using the four microsatellite markers of this study (). Since trait plasticity was calculated as the difference of trait values measured for a single genotype grown in different growth […]


Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa

BMC Genet
PMCID: 5883395
PMID: 29614950
DOI: 10.1186/s12863-018-0607-x

[…] alyses of pairwise relatedness according to Lynch and Ritland (rLR) [] were conducted with Genalex 6.4 []. Mean and 95% CI of rLR (jack-knifed over loci) for groups of individuals were estimated with Spagedi []. Mean and 95% CI for rLR between groups within prides, i.e. between males and females and between young and old animals, were estimated using the individual pairwise rLR values, each with e […]


Association Mapping for Important Agronomic Traits in Safflower (Carthamus tinctorius L.) Core Collection Using Microsatellite Markers

Front Plant Sci
PMCID: 5885069
PMID: 29651296
DOI: 10.3389/fpls.2018.00402

[…] elative probabilities of identity in descent for random genes between two individuals, i and j. Kinship coefficient matrix between all pairs of accessions of the association panel was generated using SPAGeDi v 1.5 (Hardy and Vekemans, ). All the negative Fij-values were treated as zero (Hardy and Vekemans, ; Yu et al., ). The same program was used for evaluation of average kinship coefficient (Gij […]


Genetic structure of wild pea (Pisum sativum subsp. elatius) populations in the northern part of the Fertile Crescent reflects moderate cross pollination and strong effect of geographic but not environmental distance

PLoS One
PMCID: 5868773
PMID: 29579076
DOI: 10.1371/journal.pone.0194056
call_split See protocol

[…] imated based on g2 values according David [].Spatial autocorrelation analysis, inter-population pairwise fixation index (Fst) and population pairwise distance matrix calculations were performed using SPAGeDi 1.5. To avoid overloading computing capacities, randomly chosen 4000 SNPs were selected from the dataset. Pairwise kinship coefficients [] were computed for 20 distance classes which had appro […]


Are patterns of fine scale spatial genetic structure consistent between sites within tropical tree species?

PLoS One
PMCID: 5856272
PMID: 29547644
DOI: 10.1371/journal.pone.0193501

[…] atistic ω) for S. leprosula (ω = 90.92, P < 0.001), S. parvifolia (ω = 129.88, P < 0.001) and P. tomentella (ω = 101.46, P < 0.001). Significant differences in pair-wise kinship F [] calculated using SPAGeDi were detected to a DistF of 25m in S. leprosula and S. parvifolia (P < 0.05) (, ). Within the smallest distance class, 0–25m, kinship values ranged from F = 0.058 in S. leprosula to F = 0.094 […]


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SPAGeDi institution(s)
Laboratoire de Génétique et Ecologie végétales, Université Libre de Bruxelles, Bruxelles, Belgium

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