Last update: May 25, 2024, Contributors: Dominik Schrempf, Jana Trifinopoulos, Meaningseeking, Minh Bui, Thomaskf
For advanced users to compile IQ-TREE source code.
A C++ compiler such as GCC (version >= 4.8), Clang, MS Visual Studio and Intel C++ compiler.
CMake version >= 2.8.10.
Boost library for IQ-TREE version 2. Boost library is typically available under Linux. Under MacOS you use Homebrew and run brew install boost to install the Boost library. By default IQ-TREE will detect the path to the installed Boost library.
Eigen3 library (for IQ-TREE version >= 1.6). Under MacOS you use Homebrew and run brew install eigen to install the Boost library. By default IQ-TREE will detect the path to the installed Eigen3 library. If this failed, you have to manually specify -DEIGEN3_INCLUDE_DIR=<installed_eigen3_dir> to the cmake command (see below).
OpenMP library, which is used to compile the multicore version. This should typically be the case with gcc under Linux. Under MacOS you use Homebrew and run brew install libomp to install the OpenMP library.
(Optional) Install git if you want to clone source code from IQ-TREE GitHub repository.
Choose the source code (zip or tar.gz) of the IQ-TREE release you want to use from:
https://github.com/iqtree/iqtree2/releases
For IQ-TREE version 1 please use:
https://github.com/Cibiv/IQ-TREE/releases/
Alternatively, if you have git installed, you can also clone the source code from GitHub with:
git clone --recursive https://github.com/iqtree/iqtree2.git
For IQ-TREE version 1 please clone:
git clone https://github.com/Cibiv/IQ-TREE.git
Please find below separate compilation guide fors Linux, Mac OS X, and Windows as well as for 32-bit version or for MPI version.
TIP: Ready made IQ-TREE packages are provided for Debian and Arch Linux (AUR).
Change to the source code folder:
cd PATH_TO_EXTRACTED_SOURCE_CODE
Create a subfolder, say, build and go into this subfolder:
mkdir build
cd build
Configure source code with CMake:
cmake ..
If cmake failed with message about Eigen3 not found, then install Eigen3 library and run cmake again. If this still failed, you have to manually specify the downloaded directory of Eigen3 with:
cmake -DEIGEN3_INCLUDE_DIR=<eigen3_dir> ..
Compile source code with make:
make -j
j option tells it to use all CPU cores to speed up the compilation. Without this option, make uses only one core, which might be slow.
This creates an executable iqtree2 (iqtree for version 1). It can be copied to your system search path so that IQ-TREE can be called from the Terminal simply with the command line iqtree2.
To compile IQ-TREE under Linux with ARM processor, use either GCC 10 (but not above), or Clang 14 or above.
TIP: The above guide typically compiles IQ-TREE with
gcc. If you have Clang installed and want to compile with Clang, the compilation will be similar to Mac OS X like below.
Make sure that Clang compiler is installed, which is typically the case if you installed Xcode and the associated command line tools.
If you installed cmake with Homebrew
Find the path to the CMake executable, which is typically /Applications/CMake.app/Contents/bin/cmake. For later convenience, please create a symbolic link cmake to this cmake executable, so that cmake can be invoked from the Terminal by simply entering cmake.
The steps to compile IQ-TREE are similar to Linux (see above), except that you need to specify clang as compiler when configuring source code with CMake (step 4):
cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
(please change cmake to absolute path like /Applications/CMake.app/Contents/bin/cmake).
To compile IQ-TREE under Mac with ARM processor, use Clang 17 or above.
If the OpenMP include or lib files cannot be found, then you can specify the location of OpenMP include or lib files, for example:
export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
(please change the path to the installed location of your OpenMP library)
Please first install TDM-GCC (a GCC version for Windows) from http://tdm-gcc.tdragon.net.
Then install Clang for Windows from http://clang.llvm.org.
WARNING: Although IQ-TREE can also be built with TDM-GCC, the executable does not run properly due to stack alignment issue and the
libgomplibrary causes downgraded performance for the OpenMP version. Thus, it is recommended to compile IQ-TREE with Clang.
Change to the source code folder:
cd PATH_TO_EXTRACTED_SOURCE_CODE
Please note that Windows uses back-slash (\) instead of slash (/) as path name separator.
Create a subfolder, say, build and go into this subfolder:
mkdir build
cd build
Configure source code with CMake:
cmake -G "MinGW Makefiles" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
To build the multicore version please add -DIQTREE_FLAGS=omp to the cmake command. Note that the make program shipped with TDM-GCC is called mingw32-make, thus needed to specify like above. You can also copy mingw32-make to make to simplify this step.
Compile source code with:
mingw32-make
or
mingw32-make -j4
to use 4 cores for compilation instead of only 1.
NOTE: Typically a 64-bit IQ-TREE version is built and recommended! The 32-bit version has several restriction like maximal RAM usage of 2GB and no AVX support, thus not suitable to analyze large data sets.
To compile the 32-bit version instead, simply add m32 into IQTREE_FLAGS of the cmake command:
cmake -DIQTREE_FLAGS=m32 ..
To build the 32-bit multicore version, run:
cmake -DIQTREE_FLAGS=omp-m32 ..
For Windows you need to change Clang target with:
cmake -G "MinGW Makefiles" -DCMAKE_C_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
Requirements:
Install an MPI library (e.g., OpenMPI) if not available in your system. For Mac OS X, the easiest is to install Homebrew package manager, and then install OpenMPI library from the command line with:
brew install openmpi
Then simply run CMake and make by:
cmake -DIQTREE_FLAGS=mpi ..
make -j4
IQ-TREE will automatically detect and setup the MPI paths and library. Alternatively, you can also use the MPI C/C++ compiler wrappers (typically named mpicc and mpicxx), for example:
cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx ..
make -j4
The executable is named iqtree-mpi. One can then run mpirun to start the MPI version with e.g. 2 processes:
mpirun -np 2 iqtree-mpi -s alignment ...
If you want to compile the hybrid MPI/OpenMP version, simply run:
cmake -DIQTREE_FLAGS=omp-mpi ..
make -j4
The resulting executable is then named iqtree-mpi (iqtree-omp-mpi for IQ-TREE versions <= 1.5.X). This can be used to start an MPI run with e.g. 4 processes and 2 cores each (i.e., a total of 8 cores will be used):
# For IQ-TREE version <= 1.5.X
mpirun -np 4 iqtree-omp-mpi -nt 2 -s alignment ...
# For IQ-TREE version >= 1.6.0
mpirun -np 4 iqtree-mpi -nt 2 -s alignment ...
NOTE: Please be aware that OpenMP and OpenMPI are different! OpenMP is the standard to implement shared-memory multithreading program, that we use to provide the multicore IQ-TREE version. Whereas OpenMPI is a message passing interface (MPI) library for distributed memory parallel system, that is used to compile
iqtree-mpi. Thus, one cannot runiqtreewithmpirun!
Starting with version 1.6, IQ-TREE supports Xeon Phi Knights Landing (AVX-512 instruction set). To build this version the following requirements must be met:
The compilation steps are the same except that you need to add -DIQTREE_FLAGS=KNL to the cmake command:
cmake -DIQTREE_FLAGS=KNL ..
make -j4
The compiled iqtree binary will automatically choose the proper computational kernel for the running computer. Thus, it works as normal and will speed up on Knights Landing CPUs. Run ./iqtree to make sure that the binary was compiled correctly:
IQ-TREE multicore Xeon Phi KNL version 1.6.beta for Linux 64-bit built May 7 2017
Starting with version 2.3.3, you can compile and create IQ-TREE2 lib file.
If you want to compile the IQ-TREE2 lib file, simply run:
cmake -DBUILD_LIB=ON ..
make -j4
To provide the pre-compiled IQ-TREE binaries at http://www.iqtree.org, we used Clang 3.9.0 for Windows and Clang 4.0 for Linux and macOS. We recommend to use Clang instead of GCC as Clang-compiled binaries run about 5-10% faster than GCC-compiled ones.
Linux binaries were statically compiled with Ubuntu 16.4 using libc++ library. The static-linked binaries will thus run on most Linux distributions. The CMake command is (assuming that clang-4 and clang++-4 point to the installed Clang):
# 64-bit version
cmake -DIQTREE_FLAGS=static-libcxx -DCMAKE_C_COMPILER=clang-4 -DCMAKE_CXX_COMPILER=clang++-4 <source_dir>
# 32-bit version
cmake -DIQTREE_FLAGS=static-m32 -DCMAKE_C_COMPILER=clang-4 -DCMAKE_CXX_COMPILER=clang++-4 <source_dir>
macOS binaries were compiled under macOS Sierra, but the binaries are backward compatible with Mac OS X 10.7 Lion:
cmake -DCMAKE_C_COMPILER=clang-4 -DCMAKE_CXX_COMPILER=clang++-4 <source_dir>
Windows binaries were statically compiled under Windows 7 using Clang 3.9.0 in combination with TDM-GCC 5.1.0, which provides the neccessary libraries for Clang.
# 64-bit version
cmake -G "MinGW Makefiles" -DIQTREE_FLAGS=static -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=x86_64-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
#32-bit version
cmake -G "MinGW Makefiles" -DIQTREE_FLAGS=static -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_CXX_FLAGS=--target=i686-pc-windows-gnu -DCMAKE_MAKE_PROGRAM=mingw32-make ..
Many developers in MacOS use Xcode to develop the code. To generate an XCode project for IQ-TREE, you need to run:
mkdir build-xcode
cd build-xcode
cmake -G Xcode <IQTREE_SOURCE_DIR>
This will generate a a subfolder build-xcode/iqtree.xcodeproj, which you can open in Xcode now.
Assessing Phylogenetic Assumptions
Simulating sequence alignments
Estimating amino acid substitution models
Compilation Guide