A number of software tools exist which have specific features for MAGIC-type populations. Please add to the list!
- HAPPY and instructions for application to Arabidopsis MAGIC - QTL analysis in complex crosses. Does not require pedigree information.
- genome_scan - Association mapping in Arabidopsis MAGIC. Very fast analysis of full sequence using a merge analysis approach.
- R/qtl - General QTL analysis software. Functionality for 4-way, 8-way and 16-way MAGIC.
- R/mpMap - General MAGIC software. Mainly aimed at linkage map construction. Functionality for 4-way, 8-way MAGIC (and advanced intercrosses thereof).
- R/DSPRqtl - QTL analysis in the Drosophila Synthetic Population Resource
- Churchill group - Variety of software tools, including J/qtl - GUI for R/qtl.
- Buckler group - Variety of software tools, including TASSEL and GAPIT.