physher

About physher

physher is a program for estimating evolutionary rates and divergence times from genetic, amino acid, codon, and generic data.

The current version of physher is incompatible with the first version. Documentation for installing physher1 can be found here and the manual is located here.

Getting Started

A C compiler such as gcc or clang is required. It is also requires the GSL library. On Debian-based systems, dependencies can be installed via apt:

sudo apt install gcc gsl

On MacOS, dependencies can be installed using a package manager such as Homebrew.

brew install llvm gsl

Other package managers such as conda and MacPorts can also be used to install dependencies.

Dependencies

• GSL
• sse2neon (already included in physher)

Installation

To build physher from source you can run

git clone https://github.com/4ment/physher
cmake -S physher/ -B physher/build
cmake --build physher/build/ --target install

Check install

If the installation was successful, this command should print the version of physher

physher

Building C++ wrappers (optional)

A subset of physher's functionalities is exposed in C++ wrappers. These wrappers are used in torchtree, a python program, through bindings and torchtree-physher. A C++ compiler such as g++ or clang++ is required. Compilers can be installed using apt or homebrew

git clone https://github.com/4ment/physher
cmake -S physher/ -B physher/build -DBUILD_CPP_WRAPPER=on
cmake --build physher/build/ --target install

Testing (optional)

cmake -S physher/ -B physher/build -DBUILD_TESTING=on
cmake --build physher/build/ --target install
ctest --test-dir physher/build/

Quick start

cd examples/fluA
physher JC69-time-ELBO.json

physher in action

Some examples of projects using physher

• marginal-experiments: Evaluation of 19 dubious ways to compute marginal likelihood estimates. 10.1093/sysbio/syz046.
• phylostan: Comparison of phylostan and physher using variational inference. 10.1101/702944.
• gradient-benchmark: Benchmarking of automatic differentiation and analical gradients. 10.1093/gbe/evad099
• torchtree-physher: Plugin provinding fast calculation of phylogenetic functions in physher to torchtree.

License

Distributed under the GPLv2 License. See LICENSE for more information.

Citing physher

Fourment M and Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology, 2014. doi: 10.1186/s12862-014-0163-6