cd-hit redundancy removal
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8.7 years ago
Neuls ▴ 20

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
cd-hit redundancy • 2.8k views
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You may want to check out dedupe.sh or clumpify.sh from 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.

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