cd-hit redundancy removal
I'm planing to use cd-hit to remove redundancy from a 16S mRNA dataset I have got in order to build a philogenetic tree using Phylip later on. Maybe it is a newbiew question but I wonder if i have to remove redundacy before or after doing MSA using MAFFT.
Also I wonder if the output from cd-hit can be in phylip format..
Thank you
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You may want to check out
dedupe.shorclumpify.shfrom BBMap suite for this purpose. If you are looking to remove perfectly identical reads from a NGS dataset doing it before alignments would be best.