I had bad time to do analysis for those species without ref. genome (de-novo RNA-SEQ), during these years I have experienced many tools and I think it really helps to share them, also I ask bioinformatician here to complete and suggest new tools or pipelines :
1- Blast2GO is a nice tool which performs all analysis related to GO ,pathway and even enzyme associated with De Novo RNA-SEQ transcripts,the input is transcript multiple fasta and it works slowly in trial version and you need to pay for faster version.
2-Trinotate is a protocol for functional analysis of de-novo RNA-SEQ data, this tools performs blast analysis against Swiss-Prot, Pfam, Interproscan and ..., the only problem with this tools is you should use Trinity output file as input for Trinotate.
3- My own pipeline!!: Blastx (blastx -outfmt 6 -max_target ) transcript against Swiss-Prot (downloaded from UniProt) and obtain output UniProt IDS for GO analysis by dcGO websites which tells all related GO, Pathways, disease and.., dcGO works based on protein sequence or UniProt IDS.
Please helps to expand this pipelines, because for plant biologists it is too hard to obtain functional result.