Quickstart

For Window users

IQ-TREE is a command-line program, i.e., clicking on iqtree.exe will not work. You have to open a command prompt for all analyses. As an example, if you download iqtree-1.3.10-Windows.zip into your Downloads folder, then extract it into the same folder and do the following steps:

Click on "Start" menu (below left corner of Windows screen).
Type in "cmd" and press "Enter". It will open the Command Prompt window (see Figure below).
Type in cd Downloads\iqtree-1.3.10-Windows and press "Enter" to go into IQ-TREE folder.
Optionally, type in dir to display folder content, which may look like this:

\includegraphics[width=\linewidth]{win-cmd.png}

You see that there is a bin folder (that contains the executable iqtree.exe), an example alignment file example.phy, and a manual pdf file.

Now you can try an example run by entering bin\iqtree -s example.phy.
After a few seconds, IQ-TREE finishes and you may see something like this:

\includegraphics[width=\linewidth]{win-cmd2.png}

Congratulations ;-) You have finished the first IQ-TREE analysis.

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
```