iqtreeGUI

This repository contains source code and executables for a graphical user interface for IQ-TREE.

Description

iqtreeGUI is a graphical front-end for IQ-TREE. The goal is to implement all features of IQ-TREE 1.6.* graphically. It is under active development and therefore several features are still missing (eg. a GUI for likelihood mapping, topology tests). iqtreeGUI is written in Python3 and executables are available for Windows, Linux and MacOS.

Figure: iqtreeGUi running on MacOS 10.14

Feedback appreciated

One of the great things about IQ-TREE is that is has lots of possibilities to combine different parameters and analyses. While iqtreeGUI aims to provide a graphical way to access all these features, it is almost impossible to test every possible combination of parameters IQ-TREE allows. At the moment iqtreeGUI is still under active development. Therefore there may still be a large number of bugs. I am greatful for every bug report I receive. Reporting bugs will help to improve iqtreeGUI.

Features

iqtreeGUI aims to implement all features of IQ-TREE v1.6. It has been tested with v1.6.9 but it may also run with newer versions of IQ-TREE.

Currently implemented features:

loading alignment files, creating partitions
specify models for each partition (at the moment only for DNA and AA alignments)
perform bootstrap resampling (different settings)
advanced IQ-TREE settings (starting tree, outgroup, prefix, etc.)
advanced model selection settings
advanced tree search settings (no. of starting trees, no. of iterations, ...)
advanced bootstrap settings
creating consensus trees
calculate Robinson-Foulds distances
generate random trees

Special features of iqtreeGUI:

load and save configured analyses as XML files for maximum reproducibility

Obtaining and configuring iqtreeGUI

Packaged releases:

Get the latest release here. For iqtreeGUI to work you will also need to download and install IQ-TREE.

Once you have started iqtreeGUI you will have to set the correct path to the IQ-TREE executable. Click on iqtreeGUI -> GUI settings and select the iqtree executable.

Source code:

If you would like to try the latest version of iqtreeGUI with additional features (and maybe additional bugs), you can also download the complete source code:

git clone https://github.com/reslp/iqtreeGUI

This will download the complete iqtreeGUI repository, meaning that it will download the most recent version of iqtreeGUI. You can then start iqtreeGUI directly from the newly downloaded directory:

python iqtreegui.py

Note: iqtreeGUI needs Python3 (tested with v.3.6.8). I recommend installing it with Anaconda.

Building executables

Note: These builing instructions are probably outdated and may not work. I will update them soon.

Prerequisites to build from source:

MacOS X, Linux or Windows operating system
python 3.6+, which comes with most Unix like systems
pyinstaller v3.4, for creating the executable
git

On MacOS you may execute the build_all.sh script to build iqtreeGUI for Linux, Windows and MacOS.

Building iqtreeGUI locally from source:

Make sure to install and configure pyinstaller correctly for your operating system: pyinstaller install instructions

Clone repository: git clone https://github.com/reslp/iqtreegui

The cloned repository already contains everything you need and if you have python installed you may execute iqtreegui with the command: python iqtreegui.py

To create a stand-alone executable of iqtreegui use pyinstaller: pyinstaller iqtreegui.spec for the Linux and Windows version pyinstaller iqtreegui_mac.spec for the Mac version

Compile Linux and Windows version with Docker on Mac:

If you have Docker installed you can also compile the Linux and Windows versions within a Docker container:

First you have to install the appropriate container: docker pull cdrx/pyinstaller-linux:python3 or docker pull cdrx/pyinstaller-windows:python3
Clone repository: git clone https://github.com/reslp/iqtreegui
Compile the desired version of iqtreeGUI by executing this in the iqtreeGUI source directory: docker run -v "$(pwd):/src/" cdrx/pyinstaller-linux:python3 "apt-get update -y && apt-get install -y python3-tk && pyinstaller --clean -y --dist ./dist/linux --workpath /tmp *.spec" or docker run -v "$(pwd):/src/" cdrx/pyinstaller-windows:python3

How to cite?

A manuscript is in preparation.

LICENSE

iqtreeGUI a graphical user interface for IQ-TREE

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.