MIAO-ORF: Mixture-aware Inference of Alternative-frame ORFs
MIAO (Mixture-aware Inference of Alternative-frame ORFs) detects translated alternative-frame internal open reading frames (intORFs) from ribosome-profiling data. Its codon-level Dirichlet–multinomial model tests whether phase counts are better explained by host-CDS translation alone or by a mixture of host and alternative-frame translation, and estimates the intORF-like mixture fraction, λ. The software also provides sample-level calibration, quality-control gates, model-allocated intORF abundance in pFPKM, reproducibility summaries, auditable Ribo-TISH offset import and optional codon-level P-site export. This archive corresponds to the first public release, v1.0.0, whose statistical engine and formal thresholds are locked to the 520-pair dual-background benchmark. The Zenodo deposit contains a single source ZIP for long-term software preservation. The installable wheel, source distribution, documentation and issue tracker are available from the GitHub release: https://github.com/HaomiaoSu/MIAO-ORF/releases/tag/v1.0.0.