Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications.

@article{Kenney2012HessianCF,
  title={Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications.},
  author={Toby Kenney and Hong Gu},
  journal={Statistical applications in genetics and molecular biology},
  year={2012},
  volume={11 4},
  pages={Article 14}
}
We analytically derive the first and second derivatives of the likelihood in maximum likelihood methods for phylogeny. These results enable the Newton-Raphson method to be used for maximising likelihood, which is important because there is a need for faster methods for optimisation of parameters in maximum likelihood methods. Furthermore, the calculation of the Hessian matrix also opens up possibilities for standard likelihood theory to be applied, for inference in phylogeny and for model… CONTINUE READING