File List
Here is a list of all documented files with brief descriptions:
[detail level 12]
 o*alignment.cCollection of routines for reading alignments
 o*evaluateGenericSpecial.cFunctions for computing the log likelihood at a given branch of the tree (i.e. a virtual root that is placed at this branch)
 o*genericParallelization.cGeneric master-worker parallelization with either pthreads or MPI
 o*makenewzGenericSpecial.cBranch length optimization
 o*models.cModel related code
 o*newick.cCollection of routines for reading and parsing newick trees
 o*newviewGenericSpecial.cFunctions that deal (mostly) with conditional likelihood (re)computation
 o*optimizeModel.cModel optimization routines
 o*pll.hData structures for tree and model
 o*recom.cFunctions used for recomputation of vectors (only a fraction of LH vectors stored in RAM)
 o*searchAlgo.cCollection of routines for performing likelihood computation and branch optimization
 o*topologies.cMiscellanous functions working with tree topology
 \*utils.cMiscellaneous general utility and helper functions