TASSEL specifications

Information


Unique identifier OMICS_08865
Name TASSEL
Alternative name Trait Analysis by aSSociation, Evolution and Linkage
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 5.0
Stability Stable
Requirements Java
Maintained Yes

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Maintainer


  • person_outline Peter Bradbury <>

TASSEL article

TASSEL citations

 (22)
2017
PMCID: 5431535

[…] (h e) of each population. the fixation index (f st) for each pairwise comparison was also estimated using arlequin. in addition, to characterize the genome-wide pattern of genetic variation, the tassel v5.2.3157 program was used to estimate nucleotide diversity (π) and tajima’s d value at each snp for all individuals, and the arlequin 3.5 program was used to estimate expected heterozygosity […]

2017
PMCID: 5435991

[…] the same sample size as nats., drought-induced nat pairs in a panel of 368 maize inbred lines (66) were investigated for association with drought survival (67), kernel oil content (66) and days to tassel (68). for this analysis, we used the mixed linear model and general linear model in tassel v3.0 (69). kernel oil concentration (66) and days to tassel (68) were measured under normal […]

2016
PMCID: 5217118

[…] in a final count of 2977 high-quality markers for mapping. parental allele assignment and imputation were performed using the window ld function of fsfhap (swarts et al. 2014) incorporated into tassel 5.0., linkage map construction was performed in r/qtl (r foundation for statistical computing) using the 2977 polymorphic, high-quality snp markers obtained from gbs (supplemental material, […]

2016
PMCID: 5069220

[…] asian cultivated rice (indica and japonica) was also observed, which actually also consistent with the clusters in nuclear genome test.fig. 3 , pca using the whole variation data was conducted in tassel, with the first two pcs explaining more than 81.9 % of the proportional variance; therefore, we constructed the pca using pc1 and pc2 (fig. 3c). four main groups were inferred, indica type, […]

2016
PMCID: 5047912

[…] association mapping. the loiselle algorithm was chosen for calculating the kinship matrix (k) by software spagedi (hardy and vekemans, 2002). association analysis was performed using the software tassel2. for the mixed linear model (mlm), both k and q matrices were incorporated. significance of associations between marker and traits were determined by their p values (p < 0.05), […]

TASSEL institution(s)
USA Department of Agriculture-Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, and Cisco Systems, RTP, NC, USA

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