Benjamin Wilson, Lateral GmbH, 2021.
This repository contains code to replicate the experiments reported in the paper.
The experiments ran on an Ubuntu 16 machine. Python 3.7.4, and Numpy 1.17.2 were installed via the Anaconda3-2019-10 2019.10 distribution for scientific Python. GCC version 5.4 was used (by Cython) for compilation.
The experiments should be replicable in any environment running Python >= 3.7 with a recent version of NumPy and Jupyter, and the additional software listed below.
Cython is included any Anaconda distribution, otherwise installable using pip.
If using Anaconda, both may be installed with:
conda install python-graphviz
We used the command-line binary for Linux x86, downloaded from here. This also required the installation of libpython2.7. Our Python scripts assume that the PAUP binary is available at $HOME/paup/paup, so copy it there.
Download the binary from here and copy the executables to $HOME/PhyML-3.1.
Downloaded here. We used commit 86d66160b18a4054a31b016e2d1270726775a99f (on master branch).
Obtained here or more specifically, here.
To install (you'll need make for this):
tar xvzf weighbor-1.2.tar.gz
cd Weighbor/
make
The resulting executable resided at $HOME/phylogeny/Weighbor/.
Obtained here and installed in ~/phylogeny/bionj.
Compiled with gcc BIONJ.c -o bionj.
Once Cython & GCC are installed, the Cython implementation of log-a-like (and also of hyperbolic mds) can be compiled using ./install_cythonised.