Infer approximately-maximum-likelihood phylogenetic trees.
This is a Python wrapper for FastTree.

Install using pip:

pip install git+https://github.com/iTaxoTools/FastTreePy.git

You will need a C++ compiler when building from source.

Download and run the standalone executables without installing Python.
See the latest release here.

Run the GUI:

fasttreepy-gui

Command-line tool:

fasttreepy -nt examples/simple.fas

The console tool accepts all arguments of the original program.

Run a quick analysis using defaults values:

from itaxotools.fasttreepy import quick
quick('examples/simple.fas', 'out.tre')  # save to file
quick('examples/simple.fas')  # print results

For more control over the various parameters:

from itaxotools.fasttreepy import PhylogenyApproximation
a = PhylogenyApproximation('examples/simple.fas')
a.param.sequence.ncodes = 20  # protein alignment
a.param.model.ml_model = 'wag'  # Whelan-And-Goldman
a.param.topology.mlnni = 0  # turn off min-evo NNIs and SPRs
a.launch()  # run the analysis
path = a.fetch()  # path to temporary saved results
with path.open() as file:
    print(file.read())

See itaxotools.fasttreepy.params.params for all available options.

FastTree depends on OpenMP, which is not available by default on macOS:

• Install homebrew and run brew install llvm
• In setup.py, class FastTreeExtension, change "gomp" to "omp"
• Download OpenMP from r-project: https://mac.r-project.org/openmp/
• Place the binaries and includes in ~/.local
• Run source scripts/mac/env.sh
• Install using pip

It's recommended to use PyInstaller from within a virtual environment:

git clone https://github.com/iTaxoTools/FastTreePy.git
cd FastTreePy
pip install ".[dev]"
pyinstaller scripts/fasttreepy.spec