TraitRELAX_dev_notes.txt

Added for TraitRELAX:
============================================================================
### binary substitution model with two free paprameters
/bpp-phyl/src/Bpp/Phyl/Model/TwoParameterBinarySubstitutionModel.h
/bpp-phyl/src/Bpp/Phyl/Model/TwoParameterBinarySubstitutionModel.cpp
/bpp-phyl/test/test_character_model.cpp

### implementation of the RELAX model (see: https://doi.org/10.1093/molbev/msu400)
/bpp-phyl/src/Bpp/Phyl/Model/Codon/RELAX.h
/bpp-phyl/src/Bpp/Phyl/Model/Codon/RELAX.cpp
/bpp-phyl/test/test_relax.cpp

### implementation of tree iterators in pre-order, in-order and post-order
/bpp-phyl/src/Bpp/Phyl/TreeIterator.h
/bpp-phyl/src/Bpp/Phyl/TreeIterator.cpp
/bpp-phyl/test/test_tree_iterator.cpp

### implementation of stochastic mapping (see: https://doi.org/10.1080/10635150290102393)
/bpp-phyl/src/Bpp/Phyl/Mapping/StochasticMapping.h 
/bpp-phyl/src/Bpp/Phyl/Mapping/StochasticMapping.cpp
/bpp-phyl/test/test_stochastic_mapping.cpp

### implementation of a joint likelihood of trait and branch-site models
/bpp-phyl/src/Bpp/Phyl/Likelihood/JointLikelihoodFunction.h
/bpp-phyl/src/Bpp/Phyl/Likelihood/JointLikelihoodFunction.cpp
/bpp-phyl/test/test_joint_likelihood_function.cpp

### tester for maximum parsimony implementation DRTreeParsimonyScore
/bpp-phyl/test/test_parsimony_solution.cpp


Modified for TraitRELAX:
============================================================================
### implementation of maximum parsimony using the DELTRAN approach
/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h 
/bpp-phyl/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp

### addition of a function to return the ancestral state at the root
/bpp-phyl/src/Bpp/Phyl/Simulation/DetailedSiteSimulator.h

### addition of the two-parameters binary model and the RELAX model
/bpp-phyl/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp 
/bpp-phyl/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp

### addition of the components created for TraitRELAX
/bpp-phyl/src/CMakeLists.txt