phyca

What it does

Universal single-copy orthologs (BUSCOs) are routinely used both to build deep phylogenies and to check how complete a new genome assembly is, but most existing tools treat every BUSCO gene the same way, regardless of its evolutionary history. phyca was built from a systematic analysis of over 11,000 genome assemblies across plants, fungi, and animals to change that. It identifies which BUSCO genes are prone to misidentification in a given lineage, filters those out into a Curated set (CUSCOs) that gives measurably fewer false positives, and uses that cleaner gene set to build phylogenies that hold up better against known taxonomy.

phyca also introduces a synteny-based way to compare assemblies of the same species, which gives sharper contrast between a high- and low-quality assembly than raw BUSCO completeness scores alone, useful when you're deciding which of several available assemblies for a species to actually build on. The software and the underlying database, including precomputed alignments and phylogenies for ten major eukaryotic lineages, are both public.