PedXylo: an integrated platform for autosomal and sex-linked pedigree analysis

Abstract Background Pedigree-based inference remains central to animal breeding and to conservation, evolutionary, and human-isolate research. However, existing pedigree software offers no integrated support for X-linked analysis, limited partial-decomposition functionality, no standardised pedigree-quality framework, and limited scalability to industry-sized pedigrees. Results We developed PedXylo, which extends previously published gene-dropping software for ancestral and partial inbreeding analysis into a comprehensive pedigree-analysis platform with integrated pedigree management, quality assessment, and effective-population-size estimation. PedXylo computes classical (F), Kalinowski’s new (F N ), and ancestral (F aB , F aK , AHC) inbreeding coefficients on both autosomes and the X chromosome and provides ancestor-resolved (partial) decomposition of all five coefficient families in both inheritance modes, a combination not currently available in any other tool. Pedigree quality is summarised through complete (CGE) and discrete (DGE) generation equivalents alongside two new metrics: the asymmetrical pedigree equivalents (cAPE and mAPE) and the pedigree tree imbalance (PTI). cAPE and mAPE were only weakly correlated with CGE in the European bison reference population, indicating that they capture information not represented by depth-based metrics alone. Per-individual rates of inbreeding (ΔF and ΔF X ) and effective population sizes are estimated for both autosomes and the X chromosome. We illustrate these analyses using the Habsburg lineage and a long-term captive European bison pedigree and demonstrate scalability on a 23.2-million-individual Holstein pedigree analysed in approximately 18 h on a single 40-thread workstation. Conclusions PedXylo provides a unified, scalable framework for pedigree-based inference suitable for routine application in animal breeding and applicable to wide use in conservation, evolutionary, and human-isolate research. By integrating sex-linked analysis, partial decomposition of ancestral coefficients, and new pedigree-quality metrics, it enables hypotheses that could not previously be tested with available pedigree software. The software is freely available with documentation and worked examples.