Table 2.
Summary of gene homology‐based functional prediction tools
| Tool | Description | Taxa database | Functional gene database | Functional pathway database | Link |
|---|---|---|---|---|---|
| HUMAnN3 | Profiling gene and pathway abundances with species resolution | UniRef | UniRef | MetaCyc | https://huttenhower.sph.harvard.edu/humann |
| MEGAN | Cross‐platform software for taxonomic level functionalities | NCBI taxonomy | SEED, eggNOG, KEGG, Pro2GO | https://github.com/danielhuson/megan-ce | |
| ShotMAP | ORF finding based homology inference and family classification | KEGG, FIGfams, SFams | https://github.com/sharpton/shotmap | ||
| gutSMASH | Profiling pathways for primary metabolites with strain resolution | 1621 Microbial genomes | MGCs | MGCs‐derived pathways | https://gutsmash.bioinformatics.nl/help.html#Validation |
Abbreviations: KEGG, Kyoto Encyclopedia of Genes and Genomes; MGC, metabolic gene clusters; NCBI, National Center for Biotechnology Information; ORF, open reading frame.