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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

Versioning


No version available

Maintainer


  • person_outline Peter Bradbury

Publication for Trait Analysis by aSSociation, Evolution and Linkage

TASSEL citations

 (595)
library_books

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

2018
Front Plant Sci
PMCID: 5933171
PMID: 29755499
DOI: 10.3389/fpls.2018.00561

[…] high quality SNPs with a rare allele frequency (RAF) >20% were randomly selected for the estimating panel. Based on the subgrouping results, the obtained evaluated data were used for further analysis.TASSEL 4.0 was utilized to analyze linkage disequilibrium (LD) (Bradbury et al., ), with the LD decay calculated by plotting r2 onto the genetic distance in base pairs with a cutoff of r2 = 0.2. The L […]

library_books

Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India

2018
Front Plant Sci
PMCID: 5928535
PMID: 29740461
DOI: 10.3389/fpls.2018.00520

[…] membership criterion. A principal component analysis was also used to determine population structure and used as covariate in the subsequent GWAM study. Linkage disequilibrium (LD) was estimated with Tassel software V 5.2.32 (Bradbury et al., ) using a subset of 1,577 polymorphic markers with known position selected from the original SNP marker-set. Linkage disequilibrium was calculated, using the […]

library_books

SNPversity: a web based tool for visualizing diversity

2018
PMCID: 5912076
PMID: 29688387
DOI: 10.1093/database/bay037

[…] endering, graphical representations provide quicker interpretation of information.When it comes to displaying SNP diversity, several powerful desktop software applications already exist, most notably TASSEL () and Flapjack (), but stand-alone web-based visualization tools that can be easily implemented at web-based biological databases are not common, and SNPs are usually displayed through genome […]

library_books

Genome Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)

2018
Front Plant Sci
PMCID: 5917017
PMID: 29725343
DOI: 10.3389/fpls.2018.00503

[…] In this study, we used 25,989 high-quality SNPs and indels (MAF > 0.05 and HWE > 0.001) () to perform GWAS on traits in 158 accessions. Association analyses were performed with TASSEL 5.0 () using compressed mixed linear model (MLM; P + G + Q + K) and simple model. Kinship was observed in all these SNPs. The significant association threshold was 1/n, where n is the total num […]

library_books

Genome Wide Association Study of Cadmium Accumulation at the Seedling Stage in Rapeseed (Brassica napus L.)

2018
Front Plant Sci
PMCID: 5917214
PMID: 29725340
DOI: 10.3389/fpls.2018.00375

[…] 0.75; Minor Freq > 0.05; AA, BB frequency > 0.03; GenTrain Score > 0.5) were used for population structure and relative kinship analyses as described by .The association analysis was conducted using TASSEL v. 4.0 () as well as four models: GLM, without considering Q or K; GLM, considering Q(Q); MLM, considering K(K); and MLM, considering Q and K(Q + K). The SNP markers significantly correlated wi […]

call_split

Mapping a male fertility restoration locus for the A4 cytoplasmic genic male sterility system in pearl millet using a genotyping by sequencing based linkage map

2018
BMC Plant Biol
PMCID: 5905146
PMID: 29665794
DOI: 10.1186/s12870-018-1267-8
call_split See protocol

[…] ion enzyme PstI and sequenced at 96-plex level on the Illumina HiSeq2000 with single-end read sequencing.The raw GBS data files (FASTQ) were processed to SNP calls using the GBS version 2 pipeline of Tassel 5 (Version 5.2.28) []. The sequenced tags were aligned to the pearl millet reference genomic sequence provided by the Pearl Millet Genome Sequencing Consortium [], using the Burrows-Wheeler Ali […]

Citations

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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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