PHAST

PHAST (Phylogenetic Analysis with Space/Time models) is a C-based toolkit for likelihood-based phylogenetic analysis with support for the identification of conserved elements and other large-scale comparative genomics analyses.

Building from source

PHAST now uses a standard CMake-based build system.

Dependencies

• BLAS and LAPACK
• PCRE

(Any system-provided or package-manager-provided implementations are fine.)

Build and install

cmake -S . -B build
cmake --build build
cmake --install build

By default, binaries are installed to the system prefix (e.g. /usr/local/bin or a package-manager–controlled prefix).

Multithreading Support

Uses OpenMP with 8 threads by default if found by CMake. OpenMP is not required. To set a different number of threads, update the environment variable:

export OMP_NUM_THREADS=4

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

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

Currently only phyloFit and phastCons can make use of multithreading (see -j option).

Documentation and support

For usage of individual tools, run them with –help. For questions or bug reports, please use the GitHub issue tracker.

License

PHAST is released under the BSD 3-Clause license. See LICENSE.txt for details.