I ran eggong-emapper to get the emapper.annotations file, which has the information of KEGG pathway, ko..., but how I can get the metabolism pathway and functional gene enrichment analysis. Is there any tutorial?
Have you tried DAVID? It does functional gene enrichment analysis and other interesting analysis for you.
EDIT : here you can ask for help specifically about "eggnog-mapper", maybe what you asked has been answered already.
In the original comment, I just introduced a widely used web-tools for enrichment analysis.
the input file of DAVID is a gene list, is the gene list in the emapper.annotations file? or how can i get the gene list?