BenoitMorel/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.

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