Analysis Tools - developed by Rice Diversity


Genome Browser


ALCHEMY


Plumage


GBS PLAID


Rice Sub-population Viewer

  • Description: A browsable version of the Garris et. al figure.
  • Website

Seed Photo Library Viewer

  • Description: Photo viewer of seeds in the Rice Diversity germplasm collection
  • Website

PANorama

  • Description: PANorama is a Linux-compatible, open-source software package for panicle image acquisition, processing, and phenotyping. It is available for download within the "Files" tab listed above. Installation and user instructions are within the "Wiki" tab.
  • Publication: Crowell, Samuel, Alexandre X. Falcao, Ankur Shah, Zachary Wilson, Anthony J. Greenberg, & Susan R. McCouch. (2014). High-Resolution Inflorescence Phenotyping Using a Novel Image Analysis Pipeline, PANorama. Plant Physiology (in press).
  • Download (SourceForge) Software & Documentation
  • Instructional Video PANorama: Video S1. Using GetPictures.py and ReBuildImageFiles.py [Vimeo]

Other useful analysis tools and resources

  • PLINK - whole genome association analysis toolset
  • TASSEL - evaluates linkage disequilibrium, nucleotide diversity, and trait associations
  • Flapjack - graphical genotype and haplotype visualization
  • Gramene
    • Genetic Diversity module hosts RiceDiversity datasets as they are made publicly available. Gramene hosts a wealth of information about plant genes, proteins, QTL, regulatory pathways, markers, and maps.
    • SNP Query - useful tool viewing and querying by SNP location and germplasm
    • Web launch TASSEL - Gramene Diversity data sets automatically loaded in a live-launch of TASSEL
  • BLAST - several rice genome assemblies available for BLAST analysis
  • ClustalW2 - multiple sequence alignment tool
  • r/QTL mapping script - automated QTL mapping script used in Spindel and Wright et al., 2013