phylogenetics

To perform phylogenetics, you align input sequences and infer a tree using IQ-TREE, then generate annotated figures. This end-to-end workflow handles alignment, tree inference, and visualization to reveal evolutionary relationships with sample metadata.

Yes, phylogenetic tree inference supports outbreak tracing by analyzing evolutionary relationships across aligned sequences. The workflow integrates sample metadata into annotated visualizations, enabling researchers to interpret lineage patterns during outbreaks.

IQ-TREE works within this workflow by taking prepared multiple sequence alignments as input. The process assesses sequence distances and infers trees, making it suitable for comparative genomics and evolutionary studies across diverse organisms.

The best way to visualize phylogenetic trees is using ete3 for annotated visualization. This integrates sample metadata directly into the tree figures, allowing efficient interpretation of lineage patterns for evolutionary studies.

Yes, you need aligned sequences before tree inference. The workflow first performs multiple sequence alignment and distance-based assessment to prepare data, then proceeds to infer trees with IQ-TREE and generate output artifacts.

Phylogenetic workflows are reproducible because they enforce clear tool versioning for IQ-TREE and alignment tools. This ensures end-to-end sequencing workflows produce consistent, verifiable output artifacts for evolutionary studies.