Bayesian co-estimation of phylogenies and multiple alignments via MCMC
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README.md

Build Status Appveyor

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

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

Compiling

You will need a C++ compiler that understands C++14.

  • gcc 5 (or higher) works
  • clang 3.5 (or higher) works
  • XCode 6.0 (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 >= 0.45

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 0.45, 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/
git submodule update --init   # This is optional, it allows running the testiphy testsuite

meson build --prefix=$HOME/Applications/bali-phy
ninja -C install
ninja -C 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.