phylogenetics

To build a phylogenetic tree from an unaligned FASTA file, you can automate the workflow by running sequence alignment with MAFFT, tree inference with IQ-TREE 2, and visualization with ETE3 to generate an evolutionary tree.

Automating sequence alignment and tree inference for microbial genomes is best handled by orchestrating MAFFT for alignment, IQ-TREE 2 for model selection and bootstrap support, and ETE3 to render the final phylogenetic visualization.

Yes, you can use IQ-TREE 2 and MAFFT together for end-to-end phylogenetic analysis by chaining MAFFT to align sequences and IQ-TREE 2 to infer the tree, followed by ETE3 for visualization.

Automated phylogenetic workflow orchestration handles bootstrap support and model selection by passing MAFFT alignments directly into IQ-TREE 2, which evaluates substitution models and calculates bootstrap values to ensure robust evolutionary relationships.

No, you do not need an aligned FASTA file to infer evolutionary relationships with IQ-TREE 2, because the workflow accepts unaligned FASTA input and automatically performs multiple sequence alignment using MAFFT before tree inference.

Automated phylogenetic analysis for viral phylodynamics is limited by its scope, covering typical microbial genomics and protein families, and may not handle highly divergent sequences or complex epidemiological modeling beyond standard tree inference and visualization.