Pelagibacteraceae
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Cohort-HMM marker recruitment with per-OG orthology QC for phylogenomic supermatrices
OrthoFinder's all-vs-all DIAMOND step systematically misses single-copy orthogroups (SC OGs) at deep taxonomic divergence: a marker recovered cleanly within a tightly defined cohort is dropped when the same marker is searched against phylum-broad metagenome-assembled genome (MAG) sets, because pairwise sequence similarity falls below DIAMOND's detection threshold even when the underlying ortholog is present. The result is biased dropout - supermatrices that retain genomes near the cohort but...