After qiime phylogeny filter-table does one need qiime phylogeny "filter-sequence"?

[Paul_Czechowski]

Dear Qiime develepment team,

My questions is:

• Does alignment masking remove sequences?
  • If so then running qiime phylogeny filter-table ... would be necessary, as I did it here (below).
  • If so then the unaligned sequences in the representative set need to be filtered by tree tips, the analogous command would be something like qiime phylogeny "filter-sequence" or at least filtering the rep.set by sequences in the masked alignment. But this isn’t implemnted. Is tghis a missing feature, or am I totally wrong?

I am doing this:

printf "Retaining features with tree-tips...\n"
qiime phylogeny filter-table \
  --i-table "$trpth"/"$intab" \
  --i-tree "$trpth"/"$mptpth" \
  --o-filtered-table "$trpth"/"$ottab" \
 --verbose 

• The input table is a FeatureTable
• The tree is made from a masked alignment of the representative sequences belonging to the FeatureTable

Thanks for working on Qiime a lot, please excuse my brevity. Kind regards, Paul

[gregcaporaso]

Hi @Paul_Czechowski,
Alignment masking does not remove sequences, so you don’t need to filter the table after masking.

[Paul_Czechowski]

Thank you very much for your reply. I appreciate the information very much @gregcaporaso. Kind regards, Paul