Package org.biojava.nbio.phylo

package org.biojava.nbio.phylo
  • Class
    Description
    Comparison
    This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
    DistanceMatrixCalculator
    The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
    DistanceTreeEvaluator
    Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
    ForesterWrapper
    This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
    TreeConstructor
    The TreeConstructor uses the forester library to build different types of phylogenetic trees.
    TreeConstructorType
    The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
    TreeType
    The TreeType specifies the optimization criteria used to generate the tree.