phylogenetics

To build a phylogenetic tree from unaligned FASTA sequences, the pipeline first aligns sequences using MAFFT, then infers a maximum-likelihood tree with IQ-TREE 2, and finally renders a publication-ready visualization with ETE3.

Bootstrap support in phylogenetic tree inference estimates branch reliability by resampling alignment columns. You need it to produce a defensible evolutionary tree with statistical support for outbreak or lineage interpretation.

Yes, you can use FastTree instead of IQ-TREE 2 for faster maximum-likelihood tree inference. FastTree prioritizes computational speed, whereas IQ-TREE 2 provides comprehensive model selection and bootstrap support.

Yes, this phylogenetics pipeline supports both nucleotide and protein sequence alignment. MAFFT prepares the biological sequences, allowing maximum-likelihood inference and tree visualization across both dataset types.

To root a phylogenetic tree and visualize it for publication, the pipeline uses ETE3 to compute tree statistics and apply midpoint or outgroup rooting, then renders the rooted tree structure into a PNG graphic.

Yes, you need MAFFT and IQ-TREE 2 installed separately to run this phylogenetics workflow. The pipeline requires MAFFT for sequence alignment, IQ-TREE 2 for inference, and ETE3 for rendering.