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

Original Project Page:

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/

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

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

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