Individual skill
phylogenetics
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.
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# Phylogenetics
## When to use
Use this workflow for an alignment of homologous loci or proteins, a gene tree,
branch support, and an interpretable tree figure. Multi-locus partitioning,
concordance factors, ancestral states and dating are covered in
[IQ-TREE reference](references/iqtree_inference.md).
A gene tree does not establish a species tree, transmission direction, or horizontal
transfer by itself. Sampling dates alone do not justify a molecular clock.
## Versions and installation
