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The orthologs were then aligned in MUSCLE (Edgar 2004), and codeml (Yang 2007) was implemented to measure branch lengths on all trees using a restricted tree topology with M. anisopliae and the YLS being an ingroup to N. haematococca.
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Baseball is restricted; tree climbing is not allowed.
The first stage builds a progressive alignment, the second stage that might be iterated attempts to improve the tree and builds a new progressive alignment according to this tree, and, the third stage performs iterative refinement using a variant of tree-dependent restricted partitioning.
By using a tree threaded at all levels, tree traversals for finding nearest neighbors are avoided.
Subclassification is performed using a classification tree.
The tree is constructed using a decision tree algorithm.
Finally, the "Pruning trees" tab provides an easy way to restrict tree collections by defining taxonomic filters.
A Bayesian approach does not restrict tree searches to the most parsimonious trees and allows an evolutionary model to be incorporated.
Random forest is an ensemble of classification trees that are calculated on random subsets of the data, using a subset of randomly restricted and selected predictors for each split in each classification tree.
The implementation uses a dynamic tree data structure.
We did not use a coding tree.
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