visPedigree: a comprehensive R package for tidying, analyzing, and visualizing breeding pedigrees

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ID: 322761
2026
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Abstract
Abstract Motivation Pedigrees support relatedness control, mate allocation, inbreeding monitoring and diversity assessment, but large breeding populations are often curated, analyzed and visualized using separate tools and data structures. This fragmentation complicates routine analysis and reporting, particularly in high-fecundity systems with extensive full-sib structure, irregular pedigree depth and repeated cohort-based evaluation. Results We present visPedigree, a software package for large breeding pedigrees built around a new tidyped object model. It integrates pedigree standardization, structural validation, candidate-centered tracing, pedigree statistics, inbreeding and partial inbreeding analysis, founder- and ancestor-based diversity summaries, effective population size estimation, relationship matrices and scalable visualization. The package also provides Shannon/Hill-based diversity measures, the pedhalflife() temporal diagnostic and compact visualization of full-sib-dominated subsets. In a giant freshwater prawn pedigree, it produced an interpretable ancestry overview and quantified recent diversity erosion. Simulated benchmarks showed that representative workflows completed within seconds for pedigrees containing up to one million individuals on a standard laptop. Availability and implementation visPedigree is implemented in the R language and is freely available at https://cran.r-project.org/package=visPedigree, with documentation at https://luansheng.github.io/visPedigree/.
Reference Key
openalex_W7171719337 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Sheng Luan, Jie Kong, Zhenglong Xia, Ziyi Kang, Guangfeng Qiang, Kun Luo, Juan Sui
Journal Bioinformatics advances
Year 2026
DOI
10.1093/bioadv/vbag210
URL
https://doi.org/10.1093/bioadv/vbag210
Keywords Keywords not found

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