biopython

v1.71.0

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

__init__()

Initialize the class

_get_neighbors()

Get all neighbor trees of the given tree

_nni()

Search for the best parsimony tree using the NNI algorithm

search()

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.