Package pal.tree

Class TreeDistanceMatrix

java.lang.Object
pal.distance.DistanceMatrix
pal.tree.TreeDistanceMatrix
All Implemented Interfaces:
Serializable, IdGroup

public class TreeDistanceMatrix extends DistanceMatrix
computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P. Wadell. 1998. MBE 15:1346-1359)
Version:
$Id: TreeDistanceMatrix.java,v 1.9 2002/12/05 04:27:28 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:
  • Constructor Details

    • TreeDistanceMatrix

      public TreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)
      compute induced distance matrix
      Parameters:
      idGroup - sequence order for the matrix
      t - tree
      countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)
      epsilon - minimum branch length for a which an edge is counted
    • TreeDistanceMatrix

      public TreeDistanceMatrix(Tree t, IdGroup idGroup)
      compute induced distance matrix using actual branch lengths
      Parameters:
      idGroup - sequence order for the matrix
      t - tree
    • TreeDistanceMatrix

      public TreeDistanceMatrix(Tree t, boolean countEdges, double epsilon)
      compute induced distance matrix (using tree-induced order of sequences)
      Parameters:
      t - tree
      countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)
      epsilon - minimum branch length for a which an edge is counted
    • TreeDistanceMatrix

      public TreeDistanceMatrix(Tree t)
      compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
      Parameters:
      t - tree
  • Method Details

    • recompute

      public void recompute(Tree t)