phylogenetics

To infer a phylogenetic tree, you align biological sequences using MAFFT and build evolutionary trees using IQ-TREE 2 or FastTree. This automates reconstructing evolutionary relationships to trace origins and analyze functional gene families.

The best way to align DNA, RNA, or protein sequences for evolutionary analysis is using MAFFT. Precise sequence alignment is a required prerequisite before inferring accurate phylogenetic trees with maximum likelihood methods like IQ-TREE 2.

Yes, you need to install MAFFT, IQ-TREE 2, and ETE3 to perform phylogenetic analysis. These external dependencies are required for executing sequence alignment, maximum likelihood tree building, and visualization respectively.

Use IQ-TREE 2 for robust Maximum Likelihood tree inference, or FastTree for a fast approximation. Both are supported for tree inference, letting you choose between computational precision and speed for your evolutionary analysis.

Yes, you can trace viral outbreak origins and spread using phylogenetic analysis. By aligning viral sequences with MAFFT and inferring evolutionary trees, you can facilitate molecular clock analyses and microbial genomics studies.

You visualize phylogenetic trees using ETE3. After building your evolutionary tree with IQ-TREE 2 or FastTree, the visualization component generates clear, interpretable tree representations for evolutionary studies.