Analysys Tools

Tools developed by Rice Diversity

• ALCHEMY- An automated, population genetic model driven SNP genotype calling method.
  
  • Go to the ALCHEMY Sourceforge to download software and view full documentation
  • Publication: Wright MH, et al. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 2010;26(23):2952-60.
• PANATI - Coming soon
• Rice Sub-population Viewer - A browsable version of the Garris et. al figure
• Seed Photo Library Viewer - Photo viewer of seeds in the Rice Diversity germplasm collection

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