biopython v1.71.0 Bio.Phylo.TreeConstruction.NNITreeSearcher

Tree searching with Nearest Neighbor Interchanges (NNI) algorithm.

:Parameters:

scorer : ParsimonyScorer
    parsimony scorer to calculate the parsimony score of
    different trees during NNI algorithm.

Link to this section Summary

Functions

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

Initialize the class.

Link to this function _get_neighbors()

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.