How to annotate non-model species
Take a look at EcoOmicsAnalyst
The manuscript is currently under review (preprint)
If you have already quantified your RNA-seq reads with a transcriptome that has IDs that ExpressAnalyst does not support (for example, a de novo transcriptome), you can still perform statistical analysis by leaving the organism and ID type as – Not Specified --. This will give you results in terms of your custom IDs, but you cannot perform pathway analysis.
The best option is to use EcoOmicsAnalyst for RNA-seq quantification, as Jeff has suggested.