biopython v1.71.0 Bio.Phylo.TreeConstruction.NNITreeSearcher
Tree searching with Nearest Neighbor Interchanges (NNI) algorithm.
scorer : ParsimonyScorer parsimony scorer to calculate the parsimony score of different trees during NNI algorithm.
Link to this section Summary
Link to this section Functions
Initialize the class.
Get all neighbor trees of the given tree.
Currently only for binary rooted trees.
Search for the best parsimony tree using the NNI algorithm.
Implement the TreeSearcher.search method.
:Parameters: starting_tree : Tree
starting tree of NNI method.
alignment : MultipleSeqAlignment
multiple sequence alignment used to calculate parsimony score of different NNI trees.