exporting q2 fragment insertion tree

[SoilRotifer (Mike Robeson)]

Hi @Connor_Fitzpatrick, welcome to !

This is quite similar to this thread

Remove reference tree from fragment insertion tree

Hello! I just used fragment-insertion to generate a tree following this tutorial. I used Silva 128 as a reference tree. After viewing the output in a phylogenetic tree viewer, I realized that the tree that it generates includes the entire Silva reference tree, along with all my representative sequences. Is there any way to use fragment-insertion to generate a tree with the reference tree removed, so that it only includes my representative sequences, or am I fundamentally misunderstanding how fr…

In brief you can run qiime phylogeny filter-tree ..., to remove all tips that are not represented as features in your feature table.

I'd also highly recommend q2-empress for viewing your tree. In fact, check out this YouTube video, specifically at time point 9:20, that provides a simple tutorial on empress.

-Mike