jamison413/bredelings-bali-phy

Bayesian co-estimation of phylogenies and multiple alignments via MCMC

Install

If you just want to install bali-phy, please visit the release page. If you want to compile BAli-phy from source, the quick start instructions are below.

Compiling

You will need a C++ compiler that understands C++20.

• gcc 10 (or higher) works
• clang 13 (or higher) works
• XCode 14 (or higher) works

Install Prerequisites

On Ubuntu, you can use apt-get:

sudo apt-get install g++ libcairo2-dev meson libboost-all-dev

On Mac (or Linux, actually) you can use homebrew:

brew install cairo meson boost

If the version of meson is not at least 1.0, then you need to install meson through the python package manager "pip" or "pip3":

pip3 -V
PATH=$HOME/.local/bin:$PATH
pip3 install --user meson ninja

Build BAli-Phy

git clone https://github.com/bredelings/BAli-Phy.git
cd BAli-Phy
meson build --prefix=$HOME/Applications/bali-phy
ninja -C build install
ninja -C build test

Adding bali-phy to your $PATH

In order to run the installed software, you should add bali-phy to your $PATH.

Installed locations

If you installed in $HOME/Applications/bali-phy/ as recommended above, then files will be in:

Location	Files
~/Applications/bali-phy/bin	Binary executables.
~/Applications/bali-phy/share/bali-phy/examples/sequences	Example files.
~/Applications/bali-phy/share/doc/bali-phy/	Documentation.

Further Documentation

• http://bali-phy.org/
• Manual
• Tutorial

The Manual describes how to install bali-phy in greater detail.