Filtering repseqs for a certain phylogeny

I have an environmental seawater sample with 18s genomic data. I want to filter out all sequences that are not of a specific taxa, and I have done so in the feature table using the below script.

qiime taxa filter-table
–i-table sdbaydeeuk-table.qza
–i-taxonomy sdbaydeeuk-taxonomy.qza
–p-mode exact
–p-include ‘D_0__Eukaryota;D_1__Cryptophyceae’
–o-filtered-table /home/qiime2/Desktop/qiime2/sdbaydeeuk/filtering/crypto-filtered-table.qza

Now that I have a feature table with only these sequences, I want to trim the rep-seqs file accordingly, so that when I use iTOL to visualize a phylogenetic tree I can see only the taxa of interest. However, I cannot seem to figure out how to trim the actual sequences so that all non-cryptophyceae are excluded. Any help would be appreciated, thanks!

Hi @jameshopkins,
I think what you are looking for is the filter-seqs plugin where you can use your filtered feature-table to remove sequences from your rep-seqs.

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