ImmuSeeker1.2.0

ImmuSeeker is a phylogeny-aware computational framework designed for accurate and comprehensive HLA typing from sequencing data. It addresses key limitations of existing HLA typing tools arising from the extreme sequence similarity and complex evolutionary relationships among HLA alleles. Unlike conventional approaches that focus primarily on allele identification, ImmuSeeker integrates phylogenetic information and Bayesian inference to deliver robust genotyping and zygosity estimation across multiple resolution levels. ImmuSeeker supports the extraction and quantification of HLA genotypes, gene and allele expression, and diversity metrics at the gene, one-field allele, and two-field allele levels. A Bayesian-based zygosity inference module reduces bias in heterozygosity estimation, while built-in graphical phylogenetic visualizations enable intuitive interpretation of allele relationships and typing confidence. The framework is compatible with short-read RNA-seq, long-read Iso-Seq, and longitudinal sequencing data, allowing consistent performance across diverse experimental designs. For more information, please visit the official repository at https://github.com/Limin-Jiang/ImmuSeeker.v1.2.0