How to start analysis with ASV data?

[cherman2 (Chloe Herman)]

Hi @Rishikesh12,
Unfortunately there is now way to build a phylogenetic tree in qiime2 with a feature-table collasped to the species level. If you want to do diversity analysis at the species level, you will need to run core-metrics and skip core-metrics-phylogenetic.

Here is additional information that another moderator gave when a user asked a similar question but regarding genus level analysis.

Collapsing phylogenetic tree

Hello. I collapsed my feature table using plugin qiime taxa collapse to generate genus level (level 6) feature table. Now I am trying to do beta diversity UniFrac using the genus-level feature table. However, for doing that, I need a phylogenetic tree which each label matches ID in the table. Is there any method to generate or edit (collapse) a phylogenetic tree only to contain genus level information? Thank you in advance!

Hope that helps!