pzaharias / BAli-Phy

Bayesian co-estimation of phylogenies and multiple alignments via MCMC

Install

Please visit the releases page to download official binaries.

You can also install via homebrew on a Mac, and using apt-get on recent version of Debian or Ubuntu.

Documentation

• http://bali-phy.org/
• Manual
• Tutorial
• Developer's Guide

The Manual describes how to install bali-phy in detail. Simplified instructions are below.

Compiling

You will need a C++ compiler that understands C++17.

• gcc 7 (or higher) works
• clang 7 (or higher) works
• XCode 10 (or higher) works

You will also need to install

• cairo graphics library (optional, but required to build the draw-tree program)

You will also need

• python3
• ninja
• meson >= 0.52

Install Prerequisites

sudo apt-get install g++ libcairo2-dev ninja-build python3

You also need to install meson. First try:

sudo apt-get install meson

If the version of meson is not at least 0.49, then you need to install meson through pip:

python3 -m venv meson
source meson/bin/activate
pip3 install meson

Build BAli-Phy

git clone https://github.com/bredelings/BAli-Phy.git
cd BAli-Phy
meson build --prefix=$HOME/Applications/bali-phy --buildtype=release
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.