Genomic analysis
BIGapp
A user-friendly Shiny app for genotype calling from read counts, population structure, GWAS, and genomic selection in diploid and polyploid species.
Breeding Insight mate allocation
Faster genetic gain without losing genetic diversity
AlloMate puts selection index theory and Optimum Contribution Selection (OCS) behind a code-free interface. It combines your pedigree or genomic relationships with weighted estimated breeding values (EBVs) to recommend how much each candidate should contribute to the next generation and which pairs to mate.
Access is limited to registered users. To request access, please email bi-science-team@ufl.edu.
Optimum Contribution Selection
Selecting only the candidates with the highest breeding values delivers fast gain in the short term, but top candidates are often close relatives. Using them heavily narrows the genetic base of the program and raises inbreeding in every generation that follows.
Optimum Contribution Selection decides how much each candidate should contribute to the next generation. It maximizes the expected genetic merit of the offspring while keeping their average kinship at the rate of inbreeding you choose, so you can make steady progress without losing the diversity future selection depends on.
How AlloMate works
AlloMate runs online, with no software to install and no command line. Upload your files, choose your breeding objectives, and download a mating plan. Your data is not retained: files are used only during your session and deleted when it ends.
- Candidates. Upload the list of selection candidates with their sex.
- Relationships. Upload a pedigree and AlloMate computes the kinship matrix, or upload a pedigree (A), genomic (G) or combined (H) relationship matrix, such as one from the Matrix Builder.
- Breeding values. Upload an EBV file for each trait and weight the traits to match your breeding objectives. AlloMate builds a selection index, projects the expected merit of progeny from every potential cross, and uses your kinship threshold to rule out crosses between close relatives.
- Optimum Contribution Selection. Set the desired rate of inbreeding and the number of offspring. AlloMate optimizes each candidate’s contribution to maximize genetic gain while holding inbreeding to your target and maintaining genetic diversity, then allocates matings, optionally keeping every pair below a kinship limit.
- Download your results. You receive the mating plan, optimum contributions and kinship results as an Excel workbook, or every table as tab-separated files with a record of the parameters you used.
Build relationship matrices with the Matrix Builder
The Matrix Builder computes a pedigree (A), genomic (G) or combined single-step (H) relationship matrix with the AGHmatrix package, for diploid and polyploid species. Download the matrix, or use it in place of the pedigree when you plan matings, so allocation decisions reflect the relationships your markers reveal.
More Breeding Insight tools
Breeding Insight’s open-source software covers genomic data processing, analysis and breeding data management.
Ploidy and CNV
Qploidy2
Estimates ploidy, aneuploidy, and large-scale copy number variation from genetic marker data.
R package
BIGr
Functions developed by Breeding Insight to analyze diploid and polyploid breeding and genetic data.
Panel evaluation
GenoBrew
A Shiny app for evaluating marker panel efficiency and visualizing copy number variation profiles.
Microhaplotypes
HapApp
Processes DArTag MADC reports against Breeding Insight’s public microhaplotype databases and assigns fixed allele IDs ready for downstream analysis.
Data management
DeltaBreed
Open-source breeding data management software for specialty crop and animal breeders.
Sign in with your ORCID iD to plan matings with AlloMate. AlloMate is also available as an R package you can run on your own computer; see the source code for installation instructions.