source_notes.txt

* include             A piece of the boost library.
* alignment.cpp       Managing alignments and vectors of counts.
* em.cpp              The EM algorithm, KL-divergence, likelihoods ...
* GenNon-h.cpp        The  main function.
* matrix.cpp          Matrix creation and destruction.
* miscelania.cpp, funs.cpp      Utility functions.
* model.cpp           Keeps the model dependent functions in a single place.
* model_gmm.cpp       The GMM functions.
* model_jc.cpp        The JC69 functions.
* model_k80.cpp       The K80 functions.
* model_k81.cpp       The K81 functions.
* model_ssm.cpp       The Strand-Symmetric functions.
* Newickform.cpp      Used for reading the tree  (adopted )
* parameters.cpp      Data structure for the parameters.
* random.cpp          The random generation functions, for use parameter sampling and alignment simulation.
* permutation.cpp     To create the DLC matrices.
* read_fasta.cpp      Reading the fasta files.
* sampling.cpp        Functions used for randomly sampling parameters.
* seqUtil.cpp         Used for reading the tree (adopted)
* state.cpp           Data structure for the states.
* state_list.cpp      Data structure for a list of all states in a tree (on the leaves and the hidden)
* tree.cpp            Data structure for trees (as a list of edges).

seqUtil.cpp, Newickform.cpp   modified version of the tree parser of Yu-Wei Wu (Indiana Univ), http://yuweibioinfo.blogspot.com/2008/10/newick-tree-parser-in-c-make-use-of.html