prodigal ☆
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Description:
Microbial gene prediction
Type: Formula  |  Tracked Since: Dec 28, 2025
Links: Homepage  |  formulae.brew.sh
Category: Other
Tags: bioinformatics genomics gene-prediction prokaryotes cli
Install: brew install prodigal
About:
Prodigal is a highly accurate prokaryotic gene prediction program. It identifies protein-coding sequences in bacterial and archaeal genomes by analyzing nucleotide composition and translation initiation patterns. Its main value proposition is high-speed, high-accuracy prediction suitable for large-scale metagenomic and genomic analyses.
Key Features:
  • High accuracy in identifying coding regions
  • Extremely fast processing speed
  • Ab initio gene prediction (no training data required)
  • Handles both finished and draft genomes
  • Outputs standard GFF and GenBank formats
Use Cases:
  • Annotating newly sequenced bacterial or archaeal genomes
  • Gene calling in metagenomic assemblies
  • Automated pipeline processing for large-scale genomics
Alternatives:
  • Glimmer – Glimmer is another widely used gene finder but requires a training phase, whereas Prodigal is ab initio.
  • GeneMark – GeneMark offers similar functionality but Prodigal is often preferred for its ease of use and speed on draft genomes.
Version History
Detected Version Rev Change Commit
Sep 12, 2024 7:34pm 0 VERSION_BUMP 215d78ea
Dec 2, 2022 10:19am 0 VERSION_BUMP 7b95e7a8
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