Plant Breeding, Genetics, and Genomics, just like any other scientific discipline, involves a lot of research "tools" which a breeder/geneticist can use to perform his or her analyses. Here are some of the tools that we have been using to perform genetic mapping, genome-wide predictions, and other relevant analyses on our research.

Genome-Wide Association Studies and QTL Mapping

• GAPIT

• iPAT

• TASSEL

• MapDisto

• QTL Cartographer

Genomic predictions

• iPAT

• RRBLUP

• BGLR

Genetic Diversity and Molecular Marker Analyses

• GenoDive

• STRUCTURE

• PowerMarker

• KlusterCaller

• JMP Genomics

Sample Files:

• Genotype Data

• Genotype Map Data

JMP is Your Friend:

• Part I:

• LD analysis using JMP Genomics

• Part II:

• PCA using JMP Genomics

• Part III:

• LD tag SNP selection using JMP Genomics

Phenotypic Data and Statistical Analyses

• R

• SAS

• JMP

• ACBD in R

• GEA-R

• META-R