I am working on de novo mitochondrial genome assembly of trematode species. The size of the assembled genome is ~14kb which is also expected, considering the genome size of the closest reference.
I used MITOS for gene prediction, but some of the genes are reported as split/duplicated in the result. And when the predicted split proteins (from MITOS) were aligned against the NR database using BLASTP they got aligned to the protein other than the predicted one. So I am not sure of the result and want to cross check annotation with other tools as well.
I have already tried with MITOS and DOGMA, so please let me know the names of other trematode mitochondrial genome annotation tools for gene prediction.