GeneFamHunter: annotation-independent recovery of divergent and tandemly arrayed gene-family members from genome assemblies

GeneFamHunter recovered all 130 reference papain-like (C1A) loci across six Quest for Orthologs genomes using window-based six-frame HMMER, with 21 off-target hits.

• Why it matters: Tandem duplication, divergence, and annotation errors often leave gene-family members missing or fragmented, especially in non-model organisms lacking reference proteomes.
• What they did: The method searches overlapping genomic windows across continuous six-frame translations with four complementary domain- and profile-based approaches, clusters hits to distinguish tandem paralogs, predicts/validates gene models, and builds gene trees.
• The result: Whole-contig HMMER recovered 108 (83.1%), PSI-BLAST and DELTA-BLAST recovered all loci, and across six mite genomes it recovered all 209 reported C1 loci plus 37 candidates.

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