Class Hierarchy
- java.lang.Object
- pal.alignment.AbstractAlignment (implements pal.alignment.Alignment, pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)
- pal.tree.SimulatedAlignment
- pal.tree.CladeSystem
- pal.distance.DistanceMatrix (implements pal.misc.IdGroup, java.io.Serializable)
- pal.tree.TreeDistanceMatrix
- pal.tree.Local
- pal.tree.NodeFactory
- pal.tree.NodeUtils
- pal.tree.ParameterizedTree.ParameterizedTreeBase (implements pal.misc.Parameterized, pal.tree.Tree)
- pal.tree.ClockTree (implements pal.tree.ParameterizedTree)
- pal.tree.LogParameterizedTree (implements pal.tree.ParameterizedTree)
- pal.tree.MutationRateModelTree (implements pal.math.OrthogonalHints, pal.tree.ParameterizedTree)
- pal.tree.UnconstrainedTree (implements pal.tree.ParameterizedTree)
- pal.tree.RootedTreeInterface.Utils
- pal.tree.RootedTreeUtils
- pal.tree.SimpleNode (implements pal.tree.AttributeNode)
- pal.tree.SimpleTree (implements pal.misc.Report, java.io.Serializable, pal.tree.Tree, pal.misc.Units)
- pal.tree.ClusterTree
- pal.tree.NeighborJoiningTree
- pal.tree.ReadTree
- pal.tree.UPGMATree
- pal.tree.SimulatedAlignment.Factory
- pal.tree.SplitSystem
- pal.tree.SplitUtils
- java.lang.Throwable (implements java.io.Serializable)
- java.lang.Exception
- pal.tree.TreeParseException
- java.lang.Exception
- pal.tree.Tree.TreeBase (implements pal.misc.Report, java.io.Serializable, pal.tree.Tree, pal.misc.Units)
- pal.tree.TreeGenerator.Utils
- pal.tree.TreeManipulator (implements pal.tree.RootedTreeInterface.Instructee, pal.tree.UnrootedTreeInterface.Instructee)
- pal.tree.TreeManipulator.PALBranchWrapper
- pal.tree.TreeManipulator.PALNodeWrapper
- pal.tree.TreeOperation.Utils
- pal.tree.TreeRestricter
- pal.tree.TreeTool
- pal.tree.TreeUtils
- pal.tree.UnrootedTreeInterface.Utils
- pal.alignment.AbstractAlignment (implements pal.alignment.Alignment, pal.misc.IdGroup, pal.misc.Report, java.io.Serializable)
Interface Hierarchy
- pal.tree.ClusterTree.ClusteringMethod
- pal.misc.Parameterized
- pal.tree.ParameterizedTree (also extends pal.tree.Tree)
- pal.tree.ParameterizedTree.Factory
- pal.tree.RootedTreeInterface
- pal.tree.RootedTreeInterface.Instructee
- pal.tree.RootedTreeInterface.RBranch
- pal.tree.RootedTreeInterface.RNode
- java.io.Serializable
- pal.misc.IdGroup
- pal.tree.Tree (also extends java.io.Serializable, pal.misc.Units, pal.misc.UnitsProvider)
- pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
- pal.tree.Tree (also extends java.io.Serializable, pal.misc.Units, pal.misc.UnitsProvider)
- pal.tree.Node
- pal.tree.AttributeNode
- pal.tree.Tree (also extends pal.misc.IdGroup, pal.misc.Units, pal.misc.UnitsProvider)
- pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
- pal.misc.IdGroup
- pal.tree.TreeGenerator
- pal.tree.TreeIterator
- pal.tree.TreeManipulator.BranchAccess
- pal.tree.TreeOperation
- pal.misc.Units
- pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.UnitsProvider)
- pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
- pal.misc.UnitsProvider
- pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.Units)
- pal.tree.ParameterizedTree (also extends pal.misc.Parameterized)
- pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.Units)
- pal.tree.Tree (also extends pal.misc.IdGroup, java.io.Serializable, pal.misc.UnitsProvider)
- pal.tree.UnrootedTreeInterface
- pal.tree.UnrootedTreeInterface.GeneralBranch
- pal.tree.UnrootedTreeInterface.BaseBranch
- pal.tree.UnrootedTreeInterface.UBranch
- pal.tree.UnrootedTreeInterface.Instructee
- pal.tree.UnrootedTreeInterface.UNode