sepp in R (phyloseq)

[dinhe878 (Ding He)]

Hi qiimers,

I’m getting started to dive in qiime2 world and have made some fun progress thanks to this awesome forum/community. Here I have a question regarding phylogenetic placements (sepp) viewing.

I have tried few times to view my sepp qza file at iToL website with no luck. I resorted to R phyloseq/qiime2R package but could not find a way to import sepp qza file.

Any suggestions? Any tips are appreciated!

/Ding

[SoilRotifer (Mike Robeson)]

Hi @dinhe878,

@dinhe878

I have tried few times to view my sepp qza file at iToL website with no luck.

Correct, iTOL does not play nice with fragment insertion trees. At least this has been my experience. Fortunately, there is Empress. Give that a try.

-Mike

[jbisanz (Jordan Bisanz)]

For exploratory analysis empress is probably the way to go! qiime2R should however be able to import the insertion tree, just make sure you are reading the correct artifact as there are a couple outputs if my memory is correct.