Quickstart

Minimal command-line examples

Please replace iqtree with actual path to executable:

Reconstruct maximum-likelihood tree from a sequence alignment (example.phy) with the best-fit substitution model automatically selected:
```
  iqtree -s example.phy -m TEST
```
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
```
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)

Merge partitions to reduce model complexity:

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

Perform model selection only: use -m TESTONLY or -m TESTMERGEONLY
```
  iqtree -s example.phy -sp example.nex -m TESTMERGEONLY
```
Use 4 CPU cores to speed up computation: use iqtree-omp and add -nt 4 option, e.g.:
```
  iqtree-omp -s example.phy -m TEST -alrt 1000 -bb 1000 -nt 4
```
Show all available options:
```
  iqtree -h
```