Using Mothur to analyze plant rbcl data


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,” to solve the problem?

Thanks in advance

Hi there saeedmn,

If you want to classify your rbcL sequences, you’ll have to come up with your own classification database. The files will need to follow the format in those two trainset9 files.


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