phylogenetics

To build a phylogenetic tree, you must perform multiple sequence alignment with MAFFT, infer the tree using IQ-TREE 2 or FastTree, and visualize the results with ETE3. This workflow processes DNA or protein sequences to generate rooted, supported evolutionary trees.

MAFFT is used to align DNA or protein sequences, preparing the biological data for accurate phylogenetic tree building. Proper sequence alignment is a required prerequisite before inferring maximum-likelihood trees for evolutionary research or molecular clock studies.

IQ-TREE 2 infers maximum-likelihood trees, while FastTree offers a faster approach for large-scale phylogenetic analyses. Both are supported for tree inference, allowing you to choose based on dataset size and computational needs.

ETE3 is used to visualize, root, and prune phylogenetic trees, providing clearer downstream interpretation for evolutionary research. This step is essential for interpreting the final output of your sequence alignment and tree inference workflows.

The phylogenetics workflow supports evolutionary research, microbial genomics, viral phylodynamics, protein family studies, and molecular clock analyses. It handles both small and large biological datasets across these specific domains.

FastTree is recommended for faster large-scale phylogenetic analyses, whereas IQ-TREE 2 is used for standard maximum-likelihood tree inference. The choice depends on your dataset size and the computational resources available.