phylogenetics

To build a phylogenetic tree from a FASTA file, this skill automates sequence alignment with MAFFT, infers the tree using IQ-TREE 2, and renders it via ETE3 for evolutionary analysis.

Automating sequence alignment and tree inference for viral genomes is achieved by chaining MAFFT for precise alignment and IQ-TREE 2 for maximum likelihood tree construction to map evolutionary spread.

Yes, IQ-TREE 2 and MAFFT are integrated together, aligning DNA, RNA, or protein sequences with MAFFT before inferring maximum likelihood phylogenetic trees using IQ-TREE 2.

Yes, the workflow supports protein family analysis and microbial genomics by aligning biological sequences and reconstructing evolutionary relationships to facilitate deep evolutionary studies.

To visualize a phylogenetic tree after inference, the skill uses ETE3 to render clear, interpretable tree structures directly from the generated maximum likelihood or fast approximate outputs.

You should use FastTree instead of IQ-TREE 2 when you need fast approximate phylogenetic tree inference methods, whereas IQ-TREE 2 provides maximum likelihood tree construction for precise evolutionary relationships.