@article{grantham1974amino,
  title={Amino acid difference formula to help explain protein evolution},
  author={Grantham, Richard},
  journal={Science},
  volume={185},
  number={4154},
  pages={862--864},
  year={1974},
  publisher={American Association for the Advancement of Science}
}

@article{nei1986simple,
  title={Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.},
  author={Nei, Masatoshi and Gojobori, Takashi},
  journal={Molecular biology and evolution},
  volume={3},
  number={5},
  pages={418--426},
  year={1986}
}

@article{ganeshan1997human,
  title={Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease},
  author={Ganeshan, Shanthi and Dickover, Ruth E and Korber, BT and Bryson, Yvonne J and Wolinsky, Steven M},
  journal={Journal of virology},
  volume={71},
  number={1},
  pages={663--677},
  year={1997},
  publisher={Am Soc Microbiol}
}

@article{yang2000codon,
  title={Codon-substitution models for heterogeneous selection pressure at amino acid sites},
  author={Yang, Ziheng and Nielsen, Rasmus and Goldman, Nick and Pedersen, Anne-Mette Krabbe},
  journal={Genetics},
  volume={155},
  number={1},
  pages={431--449},
  year={2000},
  publisher={Oxford University Press}
}

@article{chang2017whole,
  title={Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype},
  author={Chang, Peter L and Kopania, Emily and Keeble, Sara and Sarver, Brice AJ and Larson, Erica and Orth, Annie and Belkhir, Khalid and Boursot, Pierre and Bonhomme, Fran{\c{c}}ois and Good, Jeffrey M and others},
  journal={Mammalian Genome},
  volume={28},
  number={9},
  pages={416--425},
  year={2017},
  publisher={Springer}
}

@article{korneliussen2014angsd,
  title={ANGSD: analysis of next generation sequencing data},
  author={Korneliussen, Thorfinn Sand and Albrechtsen, Anders and Nielsen, Rasmus},
  journal={BMC bioinformatics},
  volume={15},
  number={1},
  pages={1--13},
  year={2014},
  publisher={BioMed Central}
}

@article{li1993unbiased,
  title={Unbiased estimation of the rates of synonymous and nonsynonymous substitution},
  author={Li, Wen-Hsiung},
  journal={Journal of molecular evolution},
  volume={36},
  number={1},
  pages={96--99},
  year={1993},
  publisher={Springer}
}

@article{harr2016genomic,
  title={Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus},
  author={Harr, Bettina and Karakoc, Emre and Neme, Rafik and Teschke, Meike and Pfeifle, Christine and Pezer, {\v{Z}}eljka and Babiker, Hiba and Linnenbrink, Miriam and Montero, Inka and Scavetta, Rick and others},
  journal={Scientific data},
  volume={3},
  number={1},
  pages={1--14},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{li1985new,
  title={A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.},
  author={Li, Wen-Hsiung and Wu, Chung-I and Luo, Chi-Cheng},
  journal={Molecular biology and evolution},
  volume={2},
  number={2},
  pages={150--174},
  year={1985}
}

@article{pamilo1993evolution,
  title={Evolution of the Zfx and Zfy genes: rates and interdependence between the genes.},
  author={Pamilo, Pekka and Bianchi, Nestor O},
  journal={Molecular biology and evolution},
  volume={10},
  number={2},
  pages={271--281},
  year={1993}
}

@article{tzeng2004comparison,
  title={Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions},
  author={Tzeng, Yun-Huei and Pan, Runsun and Li, Wen-Hsiung},
  journal={Molecular biology and evolution},
  volume={21},
  number={12},
  pages={2290--2298},
  year={2004},
  publisher={Society for Molecular Biology and Evolution}
}

@article{goldman1994codon,
  title={A codon-based model of nucleotide substitution for protein-coding DNA sequences.},
  author={Goldman, Nick and Yang, Ziheng},
  journal={Molecular biology and evolution},
  volume={11},
  number={5},
  pages={725--736},
  year={1994}
}

@article{zhang2006computing,
  title={Computing Ka and Ks with a consideration of unequal transitional substitutions},
  author={Zhang, Zhang and Li, Jun and Yu, Jun},
  journal={BMC evolutionary biology},
  volume={6},
  number={1},
  pages={1--10},
  year={2006},
  publisher={Springer}
}

@article{wang2009gamma,
  title={$\gamma$-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates},
  author={Wang, Da-Peng and Wan, Hao-Lei and Zhang, Song and Yu, Jun},
  journal={Biology Direct},
  volume={4},
  number={1},
  pages={1--18},
  year={2009},
  publisher={BioMed Central}
}

@article{wang2010kaks_calculator,
  title={KaKs\_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies},
  author={Wang, Dapeng and Zhang, Yubin and Zhang, Zhang and Zhu, Jiang and Yu, Jun},
  journal={Genomics, Proteomics and Bioinformatics},
  volume={8},
  number={1},
  pages={77--80},
  year={2010},
  publisher={Oxford University Press}
}
