Phylogenetic tree construction

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.

Phylogenetic tree construction involves the process of inferring evolutionary relationships among organisms or genes based on similarities and differences in their genetic sequences or other characteristics. Texasestimation suggests a methodological approach akin to assessing diverse lineages within a dataset, possibly integrating various estimation techniques or algorithms specific to phylogenetic inference. This process typically begins with aligning sequences or character data, followed by applying computational models to estimate evolutionary relationships, such as maximum likelihood or Bayesian inference.The resulting phylogenetic tree visually represents these evolutionary histories, aiding in understanding the evolutionary paths and diversification events among the taxa or genes under study.