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More Info
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DESCRIPTION
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PLATFORM
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TASSEL stands for Trait Analysis by aSSociation, Evolution and Linkage. This application evaluates linkage disequilibrium, nucleotide diversity, and trait associations. It works well with many different types of diversity data and connects to the Panzea and Gramene data repositories. It also has good graphics for LD and the ability to deal with indels for diversity analyses.
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Genomic Diversity and Phenotype Connection: 1) Front-end application allowing users to manage, retrieve, sort/group, and save/open data; 2) JAVA API for programmatic access to data sources; 3) JAVA classes to aid in development of GDPC connections to new data sources.
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Diversity Schema: Genomic Diversity and Phenotype Data Model provides a schema for holding phenotypic and genotypic data from diverse germplasm. It holds information on germplasm, field evaluations, quantitative trait values, sequence alignments from diversity surveys, SNPs, SSRs, etc.
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Field Informatics: A system with the ability to collect phenotypes quickly and accurately with little manual data entry using information-handling technologies such as bar codes and hand-held scanners. This system greatly increases the speed of data collection while minimizing human error (i.e. data entry errors and/or omission).
Also includes tools for registering plant breeding efforts, creating barcode tools and parsing barcode scanner data.
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Assorted
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Phylogeographer 1.0 is a tool for evaluating genetic and geographic interactions.
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BIOLIGN was developed by Tom Hall in consultation with this lab. This is a great tool for alignment, SNP identification, and PHRAP evaluation.
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Windows
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GAPIT, or "Genome Association and Prediction Integrated Tool," is an R package that performs Genome Wide Association Study (GWAS) and genome prediction (or selection) using state-of-the-art statistical genetics methods, including unified mixed model, EMMA, compressed mixed linear model, and P3D/EMMAx.
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R
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There are a few additional small programs and scripts here.
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