Bayesian co-estimation of phylogenies and multiple alignments via MCMC
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
doc
examples
external
functions
help
modules
python/baliphy
scripts
src
tests
.appveyor.yml
.gitignore
.gitmodules
.travis.yml
CONTRIBUTING.md
COPYING
NEWS
README.md
meson.build
meson_options.txt

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++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 >= 0.49

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
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.