MirMachine 2: a scalable, evolutionarily informed pipeline for microRNA annotation and comparative genomics across thousands of animal genomes (opens in new tab)

SUMMARY Genome sequencing is rapidly outpacing the annotation of conserved regulatory elements, limiting the evolutionary and comparative insights that can be extracted from expanding genome collections. MicroRNAs are among the most conserved and phylogenetically informative genes, yet automated annotation has remained difficult to scale while preserving evolutionary interpretability. Here we present MirMachine 2, an evolutionarily informed framework that combines curated reference models, li...