{
  "id": 19854140,
  "title": "bofasa enables high-quality orthology inference across diverse multi-species bacterial genome sets",
  "url": "https://urgent.news/2026/11/13/bofasa-enables-high-quality-orthology-inference-across-diverse-multi",
  "topic": "ai",
  "section": "AI",
  "published": "2026-11-13T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.11.11.765980v1?rss=1"
  },
  "original_language": "en",
  "account": "Bacterial species can be separated by vast stretches of time, yet studies of these ancient relationships often struggle with methods originally designed for eukaryotes. These methods can mistakenly label instances of horizontal gene transfer as contamination and struggle to handle the multi-domain architectures of some genes. To address these limitations, researchers have introduced bofasa, a software tool that excels at high-quality, automated inference of ortholog groups across distantly related bacterial species.\n\nThe innovative bofasa algorithm works by recursively splitting larger homolog groups into more focused paralogous subsets. It begins by establishing ortholog groups at the domain level before proceeding to assess evolutionary relationships between entire proteins. This approach makes bofasa a more conservative predictor of orthology compared to other methods typically used in multi-species bacterial comparative genomics. Yet, one of its standout features is its ability to often recover the largest single-copy core genome, a valuable asset for researchers studying ancient bacterial relationships.\n\nIn addition to its core orthology inference capabilities, bofasa also offers a suite of other utility functionalities. These include assessing which ortholog groups are commonly found on mobile genetic elements or possess variable genomic contexts. By providing comprehensive tools for bacterial comparative genomics across diverse multi-species genome sets, bofasa represents a significant advancement in the field.",
  "summary": "Bacterial species can be separated by billions of years of evolution. However, studies of such ancient relationships often rely on methods developed for eukaryotes, which are less diverse. Such methods can regard instances of horizontal gene transfer as contamination, rely heavily on a species phylogeny when partitioning paralogs, and fail to account for the multi-domain architectures of some…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}