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Pipeline for SNP analysis
Pipeline V2 (from Fasta)
Pipeline V3 (from VCF)
SNiPlay Galaxy workflows
Tools
General statistics
VCFtools (stats)
Polyploid analysis
SNiPloid
Chromosome Viewer
Chromosome Viewer
SNP density
Diversity analysis
EggLib
VCFtools (sliding window)
Population stratification
sNMF
Admixture
IBD Kinship (Tassel)
PCA / IBS matrix (plink)
Distance tree (FastME)
Association Studies
GWAS Analysis
Others
Cytoscape
SNP Database
Public datasets
Download public datasets
Queries
SNP Queries V3
Documentation
Manual pipeline V2
Manual pipeline V3
How to cite
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Select the database:
Coffee
Aeschynomene
Myrtaceae
Cassava_v4
Banana
Pearl_Millet
Sorghum_v3
Xanthomonas
Sorghum_v2
Meloidogyne
Cotton
Sorghum_v1
Poplar
Cassava_v6
Rice_MSU7
my_species
Magnaporthe
Microcitrus
Rice_MSU6
African_Rice
Amborella
Apple
Citrus
Chloroplast
Grapevine
Yam