Product

Everything between the field book and the breeding decision

CacaoIQ is an intelligent, AI-powered desktop application for cacao breeding programs. It reads your files, recognizes how your trial is laid out, runs a complete, documented analysis, and explains the results in plain language, in minutes to hours instead of weeks.

CacaoIQ New Analysis screen listing workflows by scientific goal, each with its pipeline steps — Choose an analysis by scientific goal. Each card shows the steps CacaoIQ will run.

End-to-end gene discovery

Input: Genotypes (SNP array, VCF or HapMap) + phenotypes

Spatially and design-corrected breeding values (BLUPs) with 95% intervals
Genomic relationship matrix and genomic heritability
Kinship-corrected GWAS with multiple-testing thresholds
For crosses with known parents: linkage map and QTL interval mapping to narrow each locus
Candidate genes around every significant locus, with a plain-language biology summary

Linkage map construction

Input: Genotypes of a full-sib family and its two parents

SNP quality control and off-type detection against the parents
Phasing and recombination-fraction estimation per chromosome
Integrated genetic map with per-chromosome lengths and marker density

Phenotypic modeling

Input: Phenotypes only, no genotype file required

Automatic model choice from your trial design (spatial, incomplete block, repeated measures)
Repeatability or broad-sense heritability, depending on how your trial is replicated
General and specific combining ability (GCA/SCA) for factorial crosses, with significance
Multi-year handling and transform suggestions for skewed traits
Trait correlation study: correlation matrices, scatter grids, boxplots and ANOVA

Trait mapping

Input: Genotypes + breeding values you have already calculated

GWAS on one trait or many, run in sequence
Every significant region clustered and searched for candidate genes
Honest handling of non-significant results: no gene lists for loci that don’t clear the threshold

Diversity panel analysis

Input: Genotypes of a germplasm collection

Population structure from principal components of the relationship matrix
Linkage-disequilibrium decay by physical distance
Neighbor-joining tree of accessions

Works with your files

CSV, TXT and Excel workbooks (pick the sheet), VCF and HapMap genotypes. Header rows, identifiers, traits and design factors are detected for you, and you can always correct the mapping.

Results you can use

Interactive charts saved as publication-ready PNGs, sortable tables exported to CSV, and a written report for each analysis, all in a folder you control.

AI that shows its work

Biology summaries are drafted by a local language model from the gene annotations shown alongside them, so every statement can be checked against its source.

Requirements

Runs on a standard laptop

One installer with everything included. No R, Python or Java to install, and no administrator terminal.

Operating system	Windows (64-bit) or macOS 13 Ventura or later on Apple silicon
Memory	16 GB recommended (8 GB minimum)
Disk space	About 10–15 GB free
Graphics card	Not required
Internet	Not required. CacaoIQ runs fully offline.

Licensed per breeding program

One license covers your core team. Get in touch for a demo and pricing for your program.