Tool stats & trends
Looking to identify usage trends or leading experts?
|Alternative name||Spatial Pattern Analysis of Genetic Diversity|
|Interface||Command line interface|
|Restrictions to use||None|
No version available
- person_outline Olivier J. Hardy
Publication for Spatial Pattern Analysis of Genetic Diversity
Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi Locus Genome Wide Association Studies
[…] ; 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
[…] 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
[…] 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
[…] 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
[…] 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?
[…] 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 […]
Looking to check out a full list of citations?
Be the first to review SPAGeDi