Now I am working with MetaPhlAn4.
I successfully made profiling file but I have faced on problem with making phylogenetic tree.
I only have its relative abundance so when I just follow the tutorial of GraphlAn, it just generated Taxonomic tree, not phylogenetic tree which shows evolutionary distance of features.
I found that there is phylogenetic tree that contains all of the SGB information, but I have no idea how to use it fro making phylogenetic tree with my data.
Anyone can give me solution or direction to solve it?
Thank you.
Hi @Jilim97
Unfortunatelly, there is not an available script in metaphlan for that task. But you could try to export the profiles in the BIOM format and run the analyses in QIIME
Constructing a phylogenetic tree from abundance data can be challenging, but with the right approach, it becomes feasible. While MetaPhlAn4 offers a strong starting point, the transition to a true phylogenetic tree requires specialized tools like FastTree or RAxML. These tools enable the conversion of abundance data into meaningful evolutionary representations, allowing you to uncover deeper insights into the relationships among features. By combining the strengths of MetaPhlAn4 with these advanced techniques, you can navigate the complexities of phylogenetic tree construction Planning and illuminate the evolutionary story within your data.