---
title: "Measuring Rearrangement Complexity in Pangenomes with the CARP Framework"
id: "biorxiv-5-quantifying-the-rearrangement-complexity-of-pangenomes"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-5-quantifying-the-rearrangement-complexity-of-pangenomes"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1?rss=1"
published_at: "2026-08-29T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Measuring Rearrangement Complexity in Pangenomes with the CARP Framework
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-5-quantifying-the-rearrangement-complexity-of-pangenomes
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1?rss=1)
- **Published At:** 2026-08-29T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors identify a gap between comparative genomics (genome rearrangement studies) and pangenomics (graphical pangenomes): both study genome evolution but use different time scales and data types, preventing a unified approach. - Classical rearrangement formulations and algorithms from comparative genomics are often unsuitable for pangenomic applications because they assume models (for example, an underlying tree) and problem sizes that many pangenomes violate. - Practical limitations include pangenomes containing so many individual genomes that NP-hard parsimony problems and all-vs-all rearrangement-distance comparisons are infeasible at scale. - Theoretical limitations include assumptions in rearrangement problem statements that are inadequate for pangenomes; these mismatches hinder direct application of existing results. - To bridge these fields, the authors propose the **Complete Ancestral Reconstruction for Pangenomes (CARP)** problem as a new formulation that overcomes listed limitations while preserving intuitive links to classical rearrangement problems and to **pangenome graphs**. - CARP is presented as retaining relationships to established rearrangement models and to the central data structures used in pangenomics, aiming to enable joint study of within- and between-species genome evolution in a unified setting. - The article is a preprint; full technical details, algorithmic formulations, empirical evaluations, and proofs were not reported in the provided source text and thus are not summarized here. - The authors declare no competing interests.
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Leonard Bohnenkaemper Bielefeld University, Faculty of Technology and Center for Biotechnology (CeBiTec) * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Leonard%2BBohnenkaemper%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Bohnenkaemper%20L&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ALeonard%2BBohnenkaemper%2B) Jens Stoye Bielefeld University, Faculty of Technology and Center for Biotechnology (CeBiTec) * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Jens%2BStoye%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Stoye%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJens%2BStoye%2B) * For correspondence: jens.stoye@uni-bielefeld.de * [Abstract](https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5740231/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5740231/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5740231/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.08.27.747493v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5740231/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract The study of evolution between species (phylogenetics) and the study of evolution within a species (population genetics) are highly related, as the same biological mechanisms are fundamental to both fields. Although both have been studied for a long time, their joint study in a unified setting has been prevented by the different time scales they consider and the different data types they employ. A similar discrepancy holds for their whole-genome specializations, comparative genomics and pangenomics. Two active areas in these fields are genome rearrangement studies and graphical pangenomics, respectively. Since the emergence of graphical pangenomics, these have existed as separate fields, despite observations that central data structures representing genomic variants in both fields are highly similar. While there exists a wealth of theoretical results for various rearrangement models in comparative genomics, the application to pangenomic data is hampered by the limitations of rearrangement problem formulations. On the practical side, pangenomes typically contain too many individual genomes for classical problems, such as the often NP-hard parsimony problems, to be solved, or for all-vs-all comparisons using rearrangement distances to be performed. On the theoretical side, some assumptions in the formulation of rearrangement problems, such as the assumption of an underlying tree, are inadequate for many pangenomes. In this work, we propose the Complete Ancestral Reconstruction for Pangenomes (CARP) problem, which overcomes these limitations while retaining intuitive relationships to both classical rearrangement problems and pangenome graphs. ### Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY 4.0 International license](http://creativecommons.org/licenses/by/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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