iqtreeGUI

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

1. 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

2. 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:

1. First you have to install the appropriate container: docker pull cdrx/pyinstaller-linux:python3 or docker pull cdrx/pyinstaller-windows:python3
2. Clone repository: git clone https://github.com/reslp/iqtreegui
3. 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

Copyright © 2019 Philipp Resl

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.