I’m using Mothur to analyze my paired-end reads data for floral composition using the rbcL gene. I made a rbcL database for taxonomic identification. The problem is in default ‘classify.seq’ command where plant sequences are tagged as unknown. What should I use instead of “reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax” to solve the problem?
Thanks in advance