• cpREV10Matrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• cpREV64Matrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• DayhoffDCMutMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• DayhoffMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• JC69Matrix : PhyloTree.SequenceSimulation.RateMatrix.DNA
• JTTDCMutMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• JTTMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• LGMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• mtArtMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• mtmamMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• mtREV24Matrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• MtZoaMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein
• RandomNumberGenerator : PhyloTree.TreeBuilding.RandomTree
• rateMLE : PhyloTree.SequenceScores.LikelihoodScores
• side1 : PhyloTree.TreeNode
• WAGMatrix : PhyloTree.SequenceSimulation.RateMatrix.Protein