Hi @Nicholas_Bokulich thank you for your response.
Regarding the Q2-ITSxpress plugin, this tutorial does not have the ITS extraction step. Apologies for my naivety as I am a newbie but is it necessary or is the trimming of the primers in this tutorial sufficient?
Thank you.
Hi @emmlemore .
The q2-itsxpress tutorial does have an ITS extraction step with the qiime itsxpress trim-pair-output-unmerged command. This tutorial does not.
They are two steps to achieve similar goals. ITSxpress trims to the ITS domain, removing the adjacent rRNA gene domains. But the primers are usually situated quite close to the ITS with only a bit of the rRNA gene domain present, so the difference is usually minimal. So which method you choose depends on your primer set and experimental goals, but both are valid options.
Good luck!
Hello everyone,
Regarding this part of the tutorial:
The comment section of the q2-ghost-tree plugin post suggests that the plugin is no longer maintained 
. Moreover, for example in this post we find some issues related with the current plugin version. In the pre-built trees GitHub repository it says that there is an issue with the UNITE database and that "the software still needs to be fixed to handle this". Pre built trees are available until UNITE v8 (v9 and 10 are currently out and in my case I'm using v10 for taxonomic classification).
My question is: anyone knows any other method for "unlocking" the use of phylogenetic methods for ITS?
Best wishes 
Thanks @salias for noting this. I have edited the original tutorial to note this for future readers (but I decided to keep the link to q2-ghosttree for posterity, in case this inspires anyone to come up with an alternative solution). My how much has changed in the past 6 years since when this tutorial was written!
I am not aware of an alternative method at the moment. But hopefully if other QIIME 2 forum members know of one they can suggest a solution.