Package org.biojava.nbio.phylo


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