Tools and Resources

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- http://www.zzlab.net/GAPIT/

• iPat- http://poissonfish.github.io/iPat/index.html

• TASSEL- https://www.maizegenetics.net/tassel

• MapDisto- http://mapdisto.free.fr/

• QTL Cartographer- https://brcwebportal.cos.ncsu.edu/qtlcart/

Genomic predictions

• iPAT- http://poissonfish.github.io/iPat/index.html

• RRBLUP- https://cran.r-project.org/web/packages/rrBLUP/index.html

• BGLR- https://cran.r-project.org/web/packages/BGLR/index.html

Genetic diversity and molecular marker analyses

• Genodive- http://www.bentleydrummer.nl/software/software/GenoDive.html (for Mac users only)

• STRUCTURE- https://web.stanford.edu/group/pritchardlab/structure.html

• PowerMarker- https://brcwebportal.cos.ncsu.edu/powermarker/

• KlusterCaller- https://www.biosearchtech.com/support/tools/genotyping-software/klustercaller

• JMP Genomics- https://www.jmp.com/en_us/software/genomics-data-analysis-software.html

  • Sample files: Genotype data; Genotype map data

  • JMP is Your Friend, Part I: LD Analysis using JMP Genomics

  • JMP is Your Friend, Part II: PCA using JMP Genomics

  • JMP is Your Friend, Part III: LD tag SNP selection using JMP Genomics

Phenotypic data and statistical analyses

• R- https://www.r-project.org/

• SAS- https://www.sas.com/en_us/home.html

• JMP- https://www.jmp.com/en_us/home.html

• ACBD in R- https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10855

• GEA-R- https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10203

• META-R- https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10201