I have a problem with reduction of redundancy from trinity output file. I have got an assembled fasta file from trinity containing 302000 contigs showing so much redundancy. I used CD_hit to remove redundancies and get unigenes. After using CD_Hit the number of contigs reduced to 240000 contigs showing lots of redundancies again. CD_Hit was not effective to achieve unigenes. Please give me advise how can I get unigens and remove redundancies?