Practical Haplotype Graph 

The Practical Haplotype Graph (PHG) is a powerful tool for representing pangenomes. The PHG is optimized for plant breeding and genetics, where genomic diversity can be high, phased haplotypes are common (e.g., inbred lines), and imputation with low-density markers is essential for breeding efficiency. This complements other imputation tools (e.g., BEAGLE) designed explicitly for handling samples from unphased species characterized by low genetic diversity and high-density genotyping.

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The PHG is a graph-based trellis representation of consecutive genic and intergenic regions (called reference ranges), representing diversity across and between samples. It can be used to:

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• Create custom genomes for alignment

• Call rare alleles

• Impute genotypes

• Efficiently store genomic data from many samples (i.e., reference, assemblies, and other lines)

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The PHG also works well with community standards, including the Breeding API (BrAPI) and efficient tools for R, such as rPHG2 for pangenome extraction and rTASSEL for connecting genotype to phenotype.