Quickstart

Minimal command-line examples (replace iqtree with actual path to executable):

1. Reconstruct maximum-likelihood tree from a sequence alignment (example.phy) with the best-fit substitution model automatically selected:

    iqtree -s example.phy -m TEST
   

2. Reconstruct ML tree and assess branch supports with ultrafast bootstrap and SH-aLRT test (1000 replicates):

    iqtree -s example.phy -m TEST -alrt 1000 -bb 1000
   

3. Perform partitioned analysis with partition definition file (example.nex) in Nexus or RAxML format using edge-linked model and gene-specific rates:

    iqtree -s example.phy -spp example.nex -m TEST
   

   (for edge-unlinked model replace -spp with -sp option)

4. Merge partitions to reduce model complexity:

    iqtree -s example.phy -sp example.nex -m TESTMERGE
   

5. Perform model selection only: use -m TESTONLY or -m TESTMERGEONLY

6. Show all available options:

    iqtree -h