Brian Kinghorn (Australia)
Likely the most utilized by industry today due to its comprehensive capabilities for mate selection and inbreeding management.
Inbreeding Management Software
Tools for managing inbreeding and optimizing mate selection
Roslin Institute
Part of the Alpha Suite for managing inbreeding in breeding programs.
Per Berg (formerly with Brian Kinghorn)
Tool for describing and optimizing selection given a penalty on rate of inbreeding.
R package for optimizing breeding schemes with consideration for inbreeding and genetic diversity.