# Install miniprot with Homebrew

Align proteins to genomes with splicing and frameshift. Version 0.18 via Homebrew; verified from local package data.

## Install

```sh
sudo av install brew:miniprot
```

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install miniprot
```

  Evidence: local Homebrew formula metadata

## Package facts

- **Package key:** brew:miniprot
- **Package manager:** Homebrew
- **Version:** 0.18
- **Source summary:** Align proteins to genomes with splicing and frameshift
- **Homepage:** <https://lh3.github.io/miniprot/>
- **Repository:** <https://github.com/lh3/miniprot>
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- miniprot (alias)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 0.18
## Project history and usage

miniprot is Heng Li's protein-to-genome aligner for genome annotation. The preprint appeared in 2022 and the Bioinformatics paper was published in 2023, describing miniprot as a new aligner for mapping protein sequences to complete genomes with k-mer sketching and vectorized dynamic programming.

### Project history

The program fills a bioinformatics gap between older tools such as GeneWise and Exonerate and the scale of modern genome projects. Its README says it aligns protein sequences against genomes with affine gap penalties, splicing, and frameshifts, primarily to annotate protein-coding genes in a new species using known genes from other species. It can build a genome index, output protein PAF, emit GFF3 with embedded PAF, and optionally use splice scores from minisplice.

### How it is used

Adoption is source-backed through bioinformatics workflows rather than general-purpose package popularity. BUSCO's user guide lists miniprot among third-party tools to cite, and the GALBA genome-annotation pipeline paper describes genome annotation with miniprot and AUGUSTUS. Homebrew packages it as a single `miniprot` executable for the scientific-command-line niche, alongside Bioconda-style distribution and upstream source builds.

### Sources

- <https://arxiv.org/abs/2210.08052>
- <https://busco.ezlab.org/busco_userguide.html>
- <https://doi.org/10.1186/s12859-023-05449-z>
- <https://formulae.brew.sh/formula/miniprot>
- <https://github.com/lh3/miniprot>
- <https://lh3.github.io/miniprot/miniprot.html>
- <https://pubmed.ncbi.nlm.nih.gov/36648328/>


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals


## Combined YAML source

View the package source record on GitHub. [combined/miniprot.yml](https://github.com/mxcl/pkgdb/blob/main/combined/miniprot.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated package history
- pkgdb category and tag curation
- cross-ecosystem install command graph