jtklein/modeltest

Best-fit model selection

ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.

Documentation

If you want to read about using ModelTest-NG, a PDF manual is attached to each release. You can also browse the wiki for online documentation, and the FAQ section for common errors.

Citation

If you use ModelTest-NG, please cite the following:

• Darriba, D., Posada, D., Kozlov, A. M., Stamatakis, A., Morel, B., & Flouri, T. (2020). ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Molecular Biology and Evolution, 37(1), 291-294. doi.org/10.1093/molbev/msz189
• Flouri T., Izquierdo-Carrasco F., Darriba D., Aberer AJ, Nguyen LT, Minh BQ, von Haeseler A., Stamatakis A. (2014) The Phylogenetic Likelihood Library. Systematic Biology, 64(2): 356-362. doi:10.1093/sysbio/syu084

Prerequisites

Core model parameter optimization and likelihood evaluation depend on the high-level modules for the Phylogenetic Likelihood Library. The latest compatible version is linked here as a submodule, so if you are cloning the repository, make sure you initialize the submodules:

$ git clone --recursive https://github.com/ddarriba/modeltest

This step is not necessary if you downloaded the released tarball.

Install

0. Automatic Build

There are 2 ways of building ModelTest-NG: - Using cmake - Using autotools

Both should work, so choose the one is more comfortable for you. If you experience any problem, please try the other one as well.

a) Build ModelTest-NG using cmake:

PTHREADS version:

```
cd modeltest-ng
mkdir build && cd build
cmake ..
make
```

MPI version:

```
cd modeltest-ng
mkdir build && cd build
cmake -DUSE_MPI=ON ..
make
```

ModelTest-NG binaries will be placed in `modeltest-ng/bin` directory.

b) Build ModelTest-NG using autotools

If you have downloaded a complete distribution, check the following files exist:
  - libpll-x.y.z.tar.gz
  - pll-modules-x.y.z.tar.gz
  - build.sh

Run the installer script:

```bash
$ build.sh
```

This should extract and compile the required libraries and link them statically
in the ModelTest-NG binaries for console (modeltest-ng, modeltest-mpi) and GUI (modeltest-gui) if
a valid `qmake` is available.

Note that, qmake might be available in some linux distributions,
but NOT a functional QT framework.
Try running `qmake`, and if you observe and error,
install `qt5-default` from apt repositories:

```bash
$ sudo apt-get install qt5-default
```

The resulting binaries and libraries will be placed in `build/bin` and `build/lib` directories

1. Graphical User Interface

To install ModelTest-NG GUI type the following commands:

$ ./build_qmake-sh
$ make -f Makefile.qmake
$ make install -f Makefile.qmake

Run 'modeltest-gui' without arguments for loading the GUI

2. Command Console Interface

To install ModelTest-NG type the following commands:

$ ./configure [--prefix=INSTALL_DIR]
$ make
$ make install

Set a custom install directory if you don't have root access or you prefer a different location.

This will compile pthreads and MPI versions Run 'modeltest-ng --help' for help about the console interface.

To compile a Windows executable, install MinGW and run:

$ ac_cv_func_malloc_0_nonnull=yes ac_cv_func_realloc_0_nonnull=yes mingw64-configure
$ make

In case the configure script does not exist, it must be generated using autotools:

$ autoreconf -i