morePhyML: improving the phylogenetic tree space exploration with PhyML 3.

@article{Criscuolo2011morePhyMLIT,
  title={morePhyML: improving the phylogenetic tree space exploration with PhyML 3.},
  author={Alexis Criscuolo},
  journal={Molecular phylogenetics and evolution},
  year={2011},
  volume={61 3},
  pages={944-8}
}
PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or "Subtree Pruning and Regrafting" (SPR) tree swapping techniques in order to find the ML phylogenetic tree. NNI-based local searches are fast but can often get trapped in local optima, whereas it is expected that the larger (but slower to cover… CONTINUE READING

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