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1. KmerGenoPhaser KmerGenoPhaser Public

   K-mer specificity + SNP/ML + autoencoder pipeline for ancestry block phasing in allopolyploid genomes. Three modules (supervised / snpml / unsupervised) + karyotype visualization. Supports sugarcan…

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2. GraphAllele GraphAllele Public

   Graph-Constrained Allele Matrix Pipeline for Polyploid Genomes

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3. LineageQuant LineageQuant Public

   Haplotype-resolved RNA-seq quantification for allopolyploid genomes via k-mer probes and EM-based read deconvolution (≥2 ancestral lineages)

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4. Hmodify Hmodify Public

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5. ATACQuant ATACQuant Public

   A k-mer-based Bayesian EM framework for quantifying subgenome-specific chromatin accessibility in polyploids

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