Practical Haplotype Graph
A pangenome database and imputation framework that represents diversity as haplotypes, making low-cost sequencing usable for genomic prediction and breeding.
TASSEL
The long-standing workhorse for association mapping of complex traits in diverse samples — GWAS, GLM/MLM, and data handling for large genotype sets.
rTASSEL
An R interface to TASSEL, bringing its association and linkage-disequilibrium engine into reproducible R workflows and pipelines.
PlantCAD
A DNA foundation model that reads genomic sequence across flowering plants — scoring evolutionary conservation and functional signal straight from DNA. PlantCAD2 spans 65 angiosperm genomes.
GeneCAD
Genome annotation with a DNA foundation model — predicting gene structure directly from sequence, without costly transcriptomic evidence, and generalizing beyond plants to animal genomes.
GAPIT
Genome Association and Prediction Integrated Tool — a widely used R package for GWAS and genomic selection with a broad menu of statistical models.
BioKotlin
A high-performance Kotlin library for computational biology, giving modern, expressive building blocks for genomic data structures and pipelines.
AnchorWave
Sensitive whole-genome alignment anchored on conserved genes — built for the deep structural diversity between plant genomes.