source_notes.txt

Source Code
----------------------------------------------------

include             A piece of the boost library.
alignment.cpp       Managing alignments and vectors of counts.
em.cpp              The EM algorithm, KL-divergence, likelihoods and much more
empar.cpp           The empar main function.
fisher.cpp          Computations of Fisher information.
matrix.cpp          Matrix creation and destruction.
miscelania.cpp      Utility functions
mixtest.cpp         The mixtest main function
model.cpp           Model dependent functions
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 SSM functions
Newickform.cpp      Read the tree
parameters.cpp      Data structure for the parameters. L2 distances, etc.
random.cpp          The random generation functions, for use in parameter sampling and alignment simulation.
read_fasta.cpp      Reading fasta files.
sampling.cpp        Functions used for random parameter sampling.
seqUtil.cpp         Used for reading the tree. Written by Yu-Wei Wu.
state.cpp           Data structure for the states.
state_list.cpp      Data structure for a list of all states in a tree (on leaves and hidden)
tree.cpp            Data structure for the trees (as a list of edges).
expm.hpp	    Matrix exponential 


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

expm.hpp Function calculating matrix exponential was adopted from: https://www.dbtsai.com/blog/2008-11-25-matrix-exponential/