Dear @thermokarst @BecksHawaii
A quick question (beginner one)
I have an OTU table (~100 rows, 9 columns) of bacterial taxa with relative abundance in two types of soils. Header like this:
| Phylum | Class | Order | Family | Genus | Species | OTU | Treatment1 | Treatment2 |
|---|---|---|---|---|---|---|---|---|
| Proteobacteria | Gammaproteobacteria | Pseudomonadales | Moraxellaceae | Acinetobacter | Acinetobacter | OTU388 | 60.15 | 39.85 |
| Actinobacteria | Actinobacteria | Micrococcales | Micrococcaceae | Pseudarthrobacter | Pseudarthrobacter | OTU872 | 55.48 | 44.52 |
I want to transform it into a “photogenic tree file” and then further annotate the tree in iTOL. I have searched and found many articles, they used MEGA, FastTree or R to prepare the tree file and used iTOL for annotation. Now I did go through the iTOL tutorial and seems pretty understandable at first look, but I do not know the how to prepare that specific tree file from an OTU table using these software. If any of you could guide me with this situation, I shall be really grateful.
*I have never used MEGA or FastTree but R.
*The photogenic Tree I want to construct is something like in this paper:
“Rhizosphere microbiome functional diversity and
pathogen invasion resistance build up during plant
development”
https://sci-hub.tw/10.1111/1462-2920.15097
If you need any information, please let me know
Khashi