Hi @jwdebelius, I want to thank you for q2-sidle, I have used it assembling sequences from six 16S regions based on SILVA 138 (release for qiime2), and the results were excellent!
However, I cannot reconstruct the phylogenetic tree, I have not been able to create or "get" an alignment of these SILVA 138 sequences. Do you have any suggestions, what could I do?
thanks
Hi @Dasiel_Obregon,
As hopefully noted in the documentation (I think it's a big note at the top of database preperation), tree building only works with the Silva 128 or Greengenes 13_8 fragment insertion trees. So, I think that's the first hurdle. Because I tend to use Silva 128, I get my alignment set from the QIIME folder on the Silva site. I'm hoping 
the next RESCRIPt release will let you reverse transcribe aligned sequences, which will solve some of the issue with RESCRIPt. I dont have a tidy solution for making a new fragment insertion backbone; I think several people have discussed it but I currently dont have the expertise or compute to do it, unfortunately.
Best,
Justine