I imported data with OTU clustering as @ [Matthew Ryan Dillon] mentioned here How to do multiplex of Ion torrent sequences - #17 by thermokarst . That's very helpful. But when I tried to generate rooted tree, it reported " The number of sequences in your feature table is larger than 1 million, please…

Hey there @nan_wang ! The parttree flag is required by mafft when there are greater than 1 million features, so it isn't an option to run mafft without. If you have questions about why that is the case I suggest you get in touch with the mafft developers. Keep us posted on what you learn! :qiime2: …

QIIME 2 Forum

The number of sequences in your feature table is larger than 1 million, please use the parttree parameter

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