I've come across several gene set enrichment tools aimed at summarizing DE genes in RNA-seq datasets, but I have a slightly different goal, and I'm wondering if any of the available tools are suitable.
I have several non-model organisms for which I've generated KEGG KO identifiers for. Instead of looking for significant differences in expression within a genome, I'm hoping to summarize significant differences between species based on KO presence/absence. For instance, one lineage has many more genes associated with flagellar function, whereas another has a more complete photosynthetic apparatus.
Maybe this question doesn't make any sense at all, but any input would be appreciated.