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
Initialize the class
Get all neighbor trees of the given tree
Search for the best parsimony tree using the NNI algorithm
Implement the TreeSearcher.search method
Link to this section Functions
Link to this function __init__()
Initialize the class.
Link to this function _get_neighbors()
Get all neighbor trees of the given tree.
Currently only for binary rooted trees.
Link to this function _nni()
Search for the best parsimony tree using the NNI algorithm.
Link to this function search()
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.