VINE

VINE (Variational Inference with Node Embeddings) is a program and set of supporting libraries for variational inference of phylogenetic trees.

Requirements

• CMake 3.x or later
• C/C++ compiler (GCC, Clang, etc.)
• PHAST (Phylogenetic Analysis with Space/Time models)

Installation

VINE is easily installable via Bioconda:

conda install -c conda-forge -c bioconda vine-phylo

or Homebrew:

brew tap CshlSiepelLab/tools
brew install vine

In both cases, PHAST will be installed as a dependency if needed.

Building from Source

If PHAST is installed in a standard location, CMake will usually find it automatically. Otherwise, you can specify its install prefix explicitly:

cmake -S . -B build \
   -DCMAKE_BUILD_TYPE=Release \
   -DPHAST_ROOT=/path/to/phast
cmake --build build
cmake --install build

Here, PHAST_ROOT should point to the installation prefix of PHAST (e.g., /opt/homebrew/opt/phast).

Multithreading Support

Uses OpenMP by default if found by CMake. OpenMP is not required.

Note for MacOS: if OpenMP is not found by default, try explicitly specifying the LLVM compiler during configuration, e.g.,

cmake -S . -B build -DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang

The number of threads can be controlled with the -j option.

Usage

For detailed usage of the main vine executable and supporting programs, run them with --help:

vine --help

The same full usage message for vine is also available directly in the source tree: vine.help_src.

Support

For questions or bug reports, please use the GitHub issue tracker.

License

Both PHAST and VINE are distributed under the BSD 3-Clause License, a permissive academic license that allows redistribution and modification provided that attribution is retained. See LICENSE for details.