Creating a phylogenetic tree for relationship between samples

General Discussion
1

Hello,

I’m wondering if anybody can tell me how to create a rooted tree for the relationship between samples. I have a rooted tree for the relationship between ASVs but I need to create a tree that can show how my samples are related to one another. Any help would be greatly appreciated.

2

Hi,
Warmly Welcome!
Please visit this page. You can find more options with their visualizations, such as alpha, beta, correlation, core-metric, etc.
I hope it helps you.
Good luck
Qiimer

3

Welcome @Sophie_Louise!

And thank you @TurboQiimer for pointing @Sophie_Louise in the right direction

More specificially, @Sophie_Louise, this action sounds like the one that you are looking for:

https://docs.qiime2.org/2020.11/plugins/available/diversity/beta-rarefaction/

Alternatively (and perhaps a little more straightforward and intuitive) would be to create a heatmap with UPGMA clustering directly on the plot:
https://docs.qiime2.org/2020.11/plugins/available/feature-table/heatmap/

Unfortunately, neither of these will output a tree that you can use in other analyses…

4

Thank you @TurboQiimer and @Nicholas_Bokulich very much for pointing me in the right direction. I really appreciate the help.

1 Like