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.

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

Reviewed against current official documentation on 2026-10-01. The executed smoke workflow used MAFFT 7.526, IQ-TREE 3.1.4, FastTree 2.2.0 and ETE3 3.1.3 on Python 3.12. ETE3 remains deliberate for this helper; ETE4 is a separate API and is not a drop-in replacement. ETE3 imports cgi, removed in Python 3.13. The native executables are not Python packages.