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https://github.com/kullrich/kakscalculator2

Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2
https://github.com/kullrich/kakscalculator2

Last synced: 4 days ago
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Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2

Host: GitHub
URL: https://github.com/kullrich/kakscalculator2
Owner: kullrich
License: gpl-3.0
Created: 2020-11-12T18:41:41.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2023-05-18T09:37:22.000Z (over 1 year ago)
Last Synced: 2023-10-20T21:04:19.322Z (about 1 year ago)
Language: C++
Size: 1.94 MB
Stars: 5
Watchers: 2
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4273737.svg)](https://doi.org/10.5281/zenodo.4273737)

[![Anaconda-Server Badge](https://anaconda.org/bioconda/kakscalculator2/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)

[![Anaconda-Server Badge](https://anaconda.org/bioconda/kakscalculator2/badges/downloads.svg)](https://anaconda.org/bioconda/kakscalculator2)

# kakscalculator2

Fork of the KaKs_Calculator2.0 project https://sourceforge.net/projects/kakscalculator2

This software is a toolkit of incorporating gamma series methods and sliding window strategies.

Original Project Admins:

[Dapeng Wang](https://sourceforge.net/u/wangdp/)

Original Project Page:

[https://sourceforge.net/projects/kakscalculator2/](https://sourceforge.net/projects/kakscalculator2/)

- only minor changes made to compile on macOS

# Building KaKs_Calculator2.0

```

git clone https://github.com/kullrich/kakscalculator2.git

export PREFIX="."

cd kakscalculator2;make clean;make

```

# Building KaKs_Calculator2.0 - Bioconda

```

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

conda install kakscalculator2

```

# Run KaKs_Calculator2.0

```

./kakscalculator2/bin/KaKs_Calculator -h

```

# Example

```

./bin/KaKs_Calculator -i ./examples/example.axt -o ./examples/example.axt.kaks -m YN

```

# Manual

```

./kakscalculator2/bin/KaKs_Calculator -h

```

see manual in KaKs_Calculator2.0.tar.gz /doc/KaKs_Calculator2.0_manual.pdf from [https://sourceforge.net/projects/kakscalculator2/](https://sourceforge.net/projects/kakscalculator2/)

# References

Wang D., Wan H-L., Zhang S., and Yu J. (2009). **γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.** *Biology Direct*, **4(20)**. [https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-20](https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-4-20)

Wang D., Zhang S., He F., Zhu J., Hu S., Yu J. (2009). **How Do Variable Substitution Rates Influence Ka and Ks Calculations?** *Genomics Proteomics Bioinformatics*, **7(3)**, 116-127. [https://dx.doi.org/10.1016/S1672-0229(08)60040-6](https://dx.doi.org/10.1016/S1672-0229(08)60040-6)

Wang D., Zhang Y., Zhang Z., Zhu J., Yu J. (2010). **KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies.** *Genomics Proteomics Bioinformatics*, **8(1)**, 77-80. [https://dx.doi.org/10.1016/S1672-0229(10)60008-3](https://dx.doi.org/10.1016/S1672-0229(10)60008-3)