Show aligned feature data


I was wondering if there is a way I can convert the alignment and masked-alignment files that are output from qiime phylogeny align-to-tree-mafft-fasttree to view them?

Thank you,

Hi @Talingar,

AFAIK, Currently there is no native way to view alignments within QIIME 2. One approach I’ve done is to export the alignment to a FASTA file and view in something like Unipro UGENE or your favorite alignment viewer.


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HI @Talingar, I was just reminded by the team that there is one little trick you can do to at least view the alignment: tabulate-seqs.


Thanks, I had tried that before (qiime feature-table tabulate-seqs --i-data alignment.qza --o-visualization --alignment.qzv) but got an error message “Invalid value for ‘–i-data’: Expected an artefact of at least type FeatureData[Sequence] . An artefact of the type FeatureData[AlignedSequence] was provided.
Do I maybe need to update my version of qiime2?


If you look at the help text by running :

qiime feature-table tabulate-seqs --help

You'll see the allowed input formats. For example, here is the allowed input for 2020.2:

and this is the allowed set of inputs for 2020.6:


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