Show aligned feature data

[Talingar]

Hi,

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,
Inga

[SoilRotifer (Mike Robeson)]

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.

-Mike

[SoilRotifer (Mike Robeson)]

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.

-Mike

[Talingar]

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?

[SoilRotifer (Mike Robeson)]

@Talingar

Do I maybe need to update my version of qiime2?

Yes.

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:

-Mike