- [MelonnPan] - [R, development] [20119.7, Nat Commun] - [Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.]
- [HUMAnN 2.0] - [Python, 最新2版v2.8.2, 2020.4] - [2018.10, Nat Methods] - [Species-level functional profiling of metagenomes and metatranscriptomes.]
- [HUMAnN 3.0] - [Python, 最新3版v3.9, 2024.2] - [2021.05, eLife] - [Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.]
- [HUMAnN 4.0] - [Python, 4.0.0.alpha.1-final, 22024.7] - [In actively development]
- [gapseq] - [R, v1.3.1, 2024.8] - [2021.3, Genome Biol] - [gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.]
- [gapseq pan] - [R, v1.3.1, 2024.8] - [2024.10, Genome Biol] - [pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.]
- Bactabolize - [Python, 1.0.4, 2024.12] - [2023.10, eLife] - [Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models]