Quickstart

Recommended for users who just downloaded IQ-TREE.

Table of Contents

Installation
For Windows users
For Mac OS X users
Minimal command-line examples

Installation

To achieve high performance IQ-TREE is a command-line program: you need to run IQ-TREE from a Terminal/Console (this is called Command Prompt under Windows). After you downloaded IQ-TREE, please:

Extract the .zip (Windows, MacOSX) or .tar.gz (Linux) file to create a directory iqtree-X.Y.Z-OS or iqtree-omp-X.Y.Z-OS.
You will find the executable in the bin sub-folder. Copy all files in bin folder to your system search path such that you can run IQ-TREE by entering iqtree or iqtree-omp from the Terminal.

Now you need to open a Terminal (or Console) to run IQ-TREE. See below the guide for Windows users and Mac OS X users.

For Windows users

Since IQ-TREE is a command-line program, clicking on iqtree.exe will not work. You have to open a Command Prompt for all analyses:

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).
Go into IQ-TREE folder you just extracted by entering e.g.:
```
 cd Downloads\iqtree-1.3.10-Windows
```
(assuming that IQ-TREE was downloaded into Downloads folder).
Now you can try an example run by entering:
```
 bin\iqtree -s example.phy
```
(example.phy is the example PHYLIP alignment file also extracted in that folder).
After a few seconds, IQ-TREE finishes and you may see something like this:

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

For Mac OS X users

Open the "Terminal", e.g., by clicking on the Spotlight icon (top-right corner), typing "terminal" and press "Enter".
Go into IQ-TREE folder by entering:
```
 cd Downloads/iqtree-1.2.0-MacOSX
```
(assuming that IQ-TREE was downloaded into Downloads folder).
Now you can try an example run by entering
```
 bin/iqtree -s example.phy
```
(example.phy is the example PHYLIP alignment file also extracted in that folder).
After a few seconds, IQ-TREE finishes and you may see something like this:

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

Minimal command-line examples

A few typically analyses are listed in the following. Note that it is assumed that iqtree executable was already copied into system search path. If not, please replace iqtree with actual path to executable.

TIP: Refer to Beginner's tutorial for more details.

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
```