bofasa enables high-quality orthology inference across diverse multi-species bacterial genome sets

bofasa enables high-quality automated orthology inference across distantly related bacterial species by using domain-level grouping and recursive paralog splitting, yielding more conservative ortholog predictions.

• Why it matters: Ancient bacterial relationships are hard to study because eukaryote-oriented orthology methods can mis-handle horizontal gene transfer, depend strongly on species phylogenies, and ignore multi-domain gene architectures.
• What they did: The software recursively partitions coarse homolog groups into paralogous subsets and first infers domain-level ortholog groups before evaluating evolutionary relationships among full proteins.
• The result: Compared with other multi-species bacterial comparative genomics tools, bofasa is substantially more conservative in orthology calls while often recovering the largest single-copy core genome, and it can also flag orthologs on mobile elements and with variable genomic contexts.

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