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https://github.com/heavywatal/tek2
🌽 Population Genetic Simulation Framework of Transposable Elements
https://github.com/heavywatal/tek2
Last synced: 7 days ago
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🌽 Population Genetic Simulation Framework of Transposable Elements
- Host: GitHub
- URL: https://github.com/heavywatal/tek2
- Owner: heavywatal
- License: mit
- Created: 2017-05-02T13:50:25.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-11-06T03:57:20.000Z (10 days ago)
- Last Synced: 2024-11-06T04:30:25.740Z (10 days ago)
- Language: C++
- Homepage: https://heavywatal.github.io/tek2/
- Size: 638 KB
- Stars: 2
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# tek2
[](https://github.com/heavywatal/tek2/actions)
*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](https://www.ncbi.nlm.nih.gov/pubmed/31580443).
[doi:10.1534/genetics.113.150292](https://doi.org/10.1093/molbev/msz220).
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](https://www.ncbi.nlm.nih.gov/pubmed/24002643).
[doi:10.1534/genetics.113.150292](http://dx.doi.org/10.1534/genetics.113.150292).
Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.
[Project page on GitHub](https://github.com/heavywatal/tek2)
## Requirements
- Unix-like environment (macOS, Linux, WSL, MinGW on MSYS2, etc.)
- C++17 compiler (clang++ >= Apple LLVM 12, g++ >= 8)
- [CMake](https://cmake.org/) (>= 3.15.0)
The following libraries are optional or automatically installed:
- [clippson](https://github.com/heavywatal/clippson)
- [cxxwtl](https://github.com/heavywatal/cxxwtl)
- [pcglite](https://github.com/heavywatal/pcglite)
- [zlib](https://zlib.net)
## Installation
The easiest way is to use [Homebrew](https://brew.sh/).
The following command installs tek2 and all the dependencies:
```sh
brew install heavywatal/tap/tek2
```
Alternatively, you can get the source code from GitHub manually:
```sh
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](https://heavywatal.github.io/tek2/)
- @ref params