phylogenetics

To build a phylogenetic tree from a FASTA file, the pipeline performs multiple sequence alignment with MAFFT, maximum-likelihood tree inference with IQ-TREE 2, and visualization with ETE3 to render the final phylogenetic results.

For phylogenetic analysis, you should use FastTree instead of IQ-TREE 2 when handling large genomic datasets. IQ-TREE 2 performs thorough maximum-likelihood model selection for smaller datasets, while FastTree provides faster inference for large-scale sequence alignments.

The best way to visualize a phylogenetic tree for publication is using ETE3 or FigTree tree-visualization tools, which render inferred maximum-likelihood phylogenetic trees into graphical outputs suitable for evolutionary studies.

No, you do not need aligned sequences to infer a phylogenetic tree. You can provide an unaligned FASTA file and the pipeline will perform multiple sequence alignment using MAFFT before inferring the tree with IQ-TREE 2.

Yes, you can use this phylogenetic pipeline for viral phylodynamics and microbial genomics. It applies maximum-likelihood phylogenetic analysis to evolutionary studies, handling datasets from small gene families to large genomic datasets.