Setting Up for IQTREE2

Getting set up for phylogenetic inference using IQTREE2 on your local machine
module 7
week 13
iqtree2
phylogenetic inference
command line
Author
Affiliation

Marguerite Butler

School of Life Sciences, University of Hawaii

Published

April 13, 2023

Acknowledgements

References for this Material:

Learning objectives

Learning objectives

At the end of this lesson you will:

  • Understand where user-installed software goes on your computer
  • Be able to install software and update the search paths to run from the command line
  • Run iqtree2 from the command line on your own computer

Overview

In the next session we will learn how to use IQTREE2 to infer phylogenetic trees (both species trees and gene trees), and compute several concordance factors. Please follow these instructions to install all of the software and ensure it is in working order before the next class. We will use R to read in and explore the output from IQTREE.

Setup iqtree software

  • Download iqtree version 2.1.2 and install the binary for your platform following the instructions below.
  • As of this writing, IQTREE2 v2.1.2 is the latest stable release version, the preview versions (e.g., 2.2.2.3) are in beta testing.
  • If you donʻt want to install IQTREE, try the webserver: http://iqtree.cibiv.univie.ac.at

Windows users

Move the IQTREE2 directory to C:\Program Files, this is where your software applicaiton files are stored. You can move it using your GUI, or using Git-Bash. Then update your computerʻs search paths so that you can run iqtree2 from the command line from any directory.

Using the GUI, Move this directory to C:\Program Files, so the path to the iqtree binary should be C:\Program Files\iqtree-2.1.2-Windows\bin\iqtree2.exe. We are writing to Program Files, which is a protected folder so it will ask you to grant Adminstrator priviledges.

OR - Using Git-Bash:

Installing Git-Bash

If you need to install Git-Bash, download it from here: https://gitforwindows.org Choose these components during installation:

  • Windows Explorer Integration
    • Git Bash Here
    • Git GUI Here
  • Git LFS
  • Associate .git* configuration files with the default text editor
  • Associate .sh files to be run with Bash
  • Add a Git Bash profile to Windows Terminal

To write files to the C:\Program Files\ directory, you will have to run Git-Bash as administrator, so do the following:

  1. Click the Windows Start button and type Git-Bash.
  2. You should see several options under Git-Bash on the right. Click on “Run as administrator”. If you donʻt see the options, click on the little “>” to the right of Git Bash, and this sub menu should appear. Use “Run as administrator”.
  3. Execute the bash commands below

Using git-bash:

Git-bash
cd Downloads
ls

Check if the directory is there an unzipped. If it is zipped, run:

Git-bash
unzip iqtree-2.1.2-Windows.zip

Move to files to the application folder. Be sure to use double quotes around the path because of the space.

Git-bash
mv iqtree-2.1.2-Windows "/C/Program Files/"

Finally, add the path to the binary to the bash search path:

Git-bash
export PATH=$PATH:"/C/Program Files/iqtree-2.1.2-Windows/bin"

Now you can just type iqtree2 from Git-bash and it should run iqtree from any folder. If you type $PATH at the command line, you should see the path you just added along with paths to many other software applications that are installed.

Mac users

Open a terminal and type $PATH. You will see the search paths that your computer looks through when you execute commands.

Terminal
$PATH

You will see the following paths, separated by :, along with many others. These are the directories that your computer searches through when you type commands on the command line searching for a match to the software you are executing.

Terminal
/opt/local/bin:/opt/local/sbin:/usr/local/bin:

If we save (a link to) the binary for IQTREE2 /opt/local/bin, then we can execute the command iqtree2 from any directory without worrying about specifying the path to the applicaiton.

Check out the directory /opt/local/. List the details of the bin subdirectory and notice that some of the applicaitons saved there are actually symbolic links

Terminal
cd /opt/local/bin
ls -la

You will see something like this, along with many other binaries:

Terminal
lrwxr-xr-x    1 root      wheel        40 Feb  7 09:30 c_rehash -> /opt/local/libexec/openssl3/bin/c_rehash
-rwxr-xr-x    1 macports  wheel  10425872 Dec 10 22:28 cmake

In the example above, c_rehash is a sybmolic link that is pointing to the location of the actual location of the binary which is in the a program directory within the libexec/ subdirectory of /opt/local. On the other hand, cmake is the binary itself.

Letʻs move the iqtree2 directory to /opt/local/libexec/. Then you will have to make a symbolic link to iqtree2 in /opt/local/bin. Start by downloading the zipped directory. It should automatically unzip. Assuming it downloaded to your Downloads folder, open a terminal and issue the following commands:

Terminal
cd ~
ls Downloads

You should see the iqtree-2.1.2-MacOSX folder inside of your Downloads folder. We will now move the iqtree folder to the place where user installed software is saved. You will probably be denied permission to just use mv folder_from folder_to because it is in a protected place on your harddrive, so you will have to use sudo for superuser do, and it will ask for your computer password to confirm.

Terminal
sudo mv Downloads/iqtree-2.1.2-MacOSX /opt/local/libexec

The directory should now be there:

Terminal
ls /opt/local/libexec

Now make a symbolic link in the /opt/local/bin folder to your iqtree executable: ln -s /path/to/original /path/to/link

Terminal
ln -s /opt/local/libexec/iqtree-2.1.2-MacOSX/bin/iqtree2 /opt/local/bin/iqtree2

If you get a permission denied, add “sudo” in front of the line to create a symbolic link. After you do that, you can just run iqtree2 on the command line from directory and it will find the app along your computerʻs searchpath. Now type iqtree2 on the command line. You should see a message like this with nine examples:

Terminal
IQ-TREE multicore version 2.1.2 COVID-edition for Mac OS X 64-bit built Oct 22 2020
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Command-line examples (replace 'iqtree2 ...' by actual path to executable):

1. Infer maximum-likelihood tree from a sequence alignment (example.phy)
   with the best-fit model automatically selected by ModelFinder:
     iqtree2 -s example.phy

2. Perform ModelFinder without subsequent tree inference:
     iqtree2 -s example.phy -m MF
   (use '-m TEST' to resemble jModelTest/ProtTest)

...

Multiple installations of iqtree2

If you want, you can install multiple versions of iqtree. Just be sure to give the binary different names. For example if you install iqtree v2.2.2.3, (latest pre-release version) you could name that binary iqtree2.2.2.3 or iqtree2beta etc. so as to have one unique name per software application.

Setup your Tutorial Folder

Make a folder for this exercise TurtleTutorial somewhere convenient (in your rclass folder?).

  • Download these files into it:

    • turtle.fa : A sequence alignment (in FASTA format) which is a subset of the original dataset used to assess the phylogenetic position of Turtles relative to Crocodiles and Birds Chiari et al., 2012.
    • turtle.nex : The partition file (in NEXUS format) defining 29 genes, which are a subset of the original dataset of 248 genes.

  • The R script concordance.R

  • The IQTREE shell script iqtreerun.sh

Test your IQTREE installation

From a terminal window, navigate to your TurtleTutorial directory and check if iqtree works:

Terminal
iqtree2
iqtree2 -s turtle.fa

It should begin running iqtree and you will see messages during execution.

R packages you will need

  • Start up R and install any necessary packages that you need to install:
    • viridis
    • GGally
    • entropy
    • ggplot2
    • dplyr
    • ggrepel

You are all set to use iqtree2!

IQTREE documentation