In the following, we describe the ingredients of the fast tree reconstruction method that are implemented in IQ-TREE. We used the phylogenetic likelihood library (Flouri et al. 2014 ) for likelihood and parsimony computations. We first describe our fast hill-climbing NNI algorithm that is repeatedly used throughout the tree search. Subsequently, we will explain the initial tree generation and the stochastic NNI process.
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Fast Tree Reconstruction with IQ-TREE
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Library
Reconstruction
Tree
Corresponding Organization :
Other organizations : Max Perutz Labs, Medical University of Vienna, University of Vienna
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Protocol cited in 5 989 other protocols
Variable analysis
independent variables
- Fast hill-climbing NNI algorithm
- Initial tree generation
- Stochastic NNI process
- Likelihood and parsimony computations
- Phylogenetic likelihood library (Flouri et al. 2014)
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