tek2

tek2 is a population genetic simulation framework of transposons.

Reference

W. M. Iwasaki, T. E. Kijima, and H. Innan (2020) Mol. Biol. Evol. 37(2):355–364. pmid:31580443. doi:10.1534/genetics.113.150292. Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily.

T. E. Kijima and H. Innan (2013) Genetics 195(3):957–967. pmid:24002643. doi:10.1534/genetics.113.150292. Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

Project page on GitHub

Requirements

• Unix-like environment (macOS, Linux, WSL, MinGW on MSYS2, etc.)
• C++17 compiler (clang++ >= Apple LLVM 12, g++ >= 8)
• CMake (>= 3.15.0)

The following libraries are optional or automatically installed:

• clippson
• cxxwtl
• sfmt-class
• zlib

Installation

The easiest way is to use Homebrew. The following command installs tek2 and all the dependencies:

brew install heavywatal/tap/tek2

Alternatively, you can get the source code from GitHub manually:

git clone https://github.com/heavywatal/tek2.git
cd tek2/
mkdir build
DESTINATION=${HOME}/local  # or /usr/local
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$DESTINATION
cmake --build build -j 2
cmake --install build -j 2
PATH=${DESTINATION}/bin:$PATH

API Document

• Online documentation generated with doxygen
• Parameters