{
  "abstract": "Gene family expansion and contraction analysis is a commonly used approach in evolutionary comparative genomics to identify lineage-specific evolutionary pressures on gene copy/family number. CAFE is one of the most popular tools to measure changes in gene family size, but requires a high level of bioinformatics expertise, manual parameter tuning and preprocessing. Here we present EXCON, an automated, Eco-Flow community-developed Nextflow pipeline that integrates NCBI genome download, annotation quality and format pre-processing, orthologous gene family identification (Orthofinder), ultrametric tree formatting, birth-death modelling (CAFE), and GO enrichment analysis (eggNOG-mapper/TopGO) into a single, portable workflow. EXCON accepts genome assemblies and annotations, supports local, HPC and cloud-based computing environments, and requires minimal user configuration. The pipeline auto-selects appropriate CAFE lambda and error models, and separates high variance orthogroups for separate treatment. Applied to a 24-species primate dataset spanning Catarrhini, Platyrrhini and Strepsirrhini, the pipeline identified 358 rapidly evolving gene families, including a DUX (double homeobox) gene showing repeated, independent copy-number turnover across multiple lineages, consistent with the known instability of the D4Z4 macrosatellite repeat it resides in. EXCON is freely available at https://github.com/Eco-Flow/excon.",
  "abstract_shown": true,
  "affiliations": [
    "University College London"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "C. D. R. Wyatt"
    },
    {
      "name": "F. Duarte"
    },
    {
      "name": "A. Cerqueira De Araujo"
    },
    {
      "name": "S. Murray"
    },
    {
      "name": "C. Oi"
    },
    {
      "name": "S. Sumner"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/0t0z8qvc6dphm.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.25.754512",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1.full",
  "id": "0t0z8qvc6dphm",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "evolutionary biology"
    ],
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7215115652",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-25",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/0t0z8qvc6dphm.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:38Z",
      "native_id": "10.64898/2026.09.25.754512",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.25.754512v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis",
  "title_text": "EXCON: a scalable, reproducible Nextflow pipeline for CAFE-based gene EXpansion and CONtraction analysis",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:38Z",
  "url": "https://research.draconitic.com/paper/0t0z8qvc6dphm",
  "venue": "bioRxiv",
  "versions": []
}