Iqtree

# 2) Tree inference with support values
iqtree -s alignment.fasta -m GTR+F+R4 -B 1000 --alrt 1000 -T AUTO

# 3) Partitioned analysis
iqtree -s alignment.fasta -p partitions.nex -m MFP -T AUTO

Recommended Workflow

1. Start from a trustworthy multiple-sequence alignment.
2. Run model selection unless a justified model is already fixed by protocol.
3. Add branch support estimation in the same run or a well-documented follow-up run.
4. Inspect .iqtree, .treefile, and support values before making biological claims.

Guardrails

• IQ-TREE does not align sequences; garbage alignments produce garbage trees.
• -B ultrafast bootstrap is intended for large replicate counts, commonly >=1000.
• Use -T AUTO and --mem thoughtfully on shared machines.
• Model choice, support values, and partition strategy are part of the inference, not optional cosmetics.