Version Compatibility

Reference examples tested with: IQ-TREE 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Modern ML Tree Inference

"Infer a maximum likelihood tree from my alignment" → Build publication-quality ML trees with automatic substitution model selection and ultrafast bootstrap support assessment.

• CLI: iqtree2 -s alignment.fa -m MFP -B 1000 (IQ-TREE2)
• CLI: raxml-ng --all --msa alignment.fa --model GTR+G --bs-trees 100 (RAxML-ng)

Build maximum likelihood phylogenetic trees with automatic model selection and ultrafast bootstrap.

IQ-TREE2 Basic Usage