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水稻遗传多样性常用分析工具:Rice Diversity Analysys Tools  

2011-10-13 22:20:15|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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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
via:http://www.ricediversity.org/tools/index.cfm
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