Stochastic search strategy for estimation of maximum likelihood phylogenetic trees.

@article{Salter2001StochasticSS,
  title={Stochastic search strategy for estimation of maximum likelihood phylogenetic trees.},
  author={Laura A. Salter and Dennis K. Pearl},
  journal={Systematic biology},
  year={2001},
  volume={50 1},
  pages={
          7-17
        }
}
The maximum likelihood (ML) method of phylogenetic tree construction is not as widely used as other tree construction methods (e.g., parsimony, neighbor-joining) because of the prohibitive amount of time required to find the ML tree when the number of sequences under consideration is large. To overcome this difficulty, we propose a stochastic search strategy for estimation of the ML tree that is based on a simulated annealing algorithm. The algorithm works by moving through tree space by way of… CONTINUE READING

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