A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

@article{Guindon2003ASF,
  title={A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.},
  author={St{\'e}phane Guindon and Olivier Gascuel},
  journal={Systematic biology},
  year={2003},
  volume={52 5},
  pages={
          696-704
        }
}
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method… 
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