# modeltest

**Repository Path**: pengfang11/modeltest

## Basic Information

- **Project Name**: modeltest
- **Description**: Best-fit model selection
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-10-06
- **Last Updated**: 2024-05-30

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

![ModelTest-NG](https://github.com/ddlsandbox/assets/blob/master/modeltest/img/header.png?raw=true)

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](https://github.com/ddarriba/modeltest/releases).
You can also browse the [wiki](https://github.com/ddarriba/modeltest/wiki) for
online documentation, and the [FAQ section](https://github.com/ddarriba/modeltest/wiki/FAQ)
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:

```bash
$ 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:

  ```bash
  $ ./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:

  ```bash
  $ ./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:

```bash
$ 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:

```bash
$ autoreconf -i
```