src Directory Reference
+ Directory dependency graph for src:

Files

file  alignment.c
 Collection of routines for reading alignments.
 
file  avxLikelihood.c
 
file  bipartitionList.c
 
file  cycle.h [code]
 
file  errcodes.h [code]
 
file  evaluateGenericSpecial.c
 Functions for computing the log likelihood at a given branch of the tree (i.e. a virtual root that is placed at this branch)
 
file  evaluatePartialGenericSpecial.c
 
file  fastDNAparsimony.c
 
file  genericParallelization.c
 Generic master-worker parallelization with either pthreads or MPI.
 
file  genericParallelization.h [code]
 
file  globalVariables.h [code]
 
file  hash.c
 
file  hash.h [code]
 
file  lexer.c
 
file  lexer.h [code]
 
file  makenewzGenericSpecial.c
 Branch length optimization.
 
file  mem_alloc.c
 
file  mem_alloc.h [code]
 
file  models.c
 Model related code.
 
file  newick.c
 Collection of routines for reading and parsing newick trees.
 
file  newick.h [code]
 
file  newviewGenericSpecial.c
 Functions that deal (mostly) with conditional likelihood (re)computation.
 
file  optimizeModel.c
 Model optimization routines.
 
file  parsePartition.c
 
file  parsePartition.h [code]
 
file  pll.h [code]
 Data structures for tree and model.
 
file  queue.c
 
file  queue.h [code]
 
file  randomTree.c
 
file  recom.c
 Functions used for recomputation of vectors (only a fraction of LH vectors stored in RAM)
 
file  restartHashTable.c
 
file  searchAlgo.c
 Collection of routines for performing likelihood computation and branch optimization.
 
file  ssort.c
 
file  stack.c
 
file  stack.h [code]
 
file  topologies.c
 Miscellanous functions working with tree topology.
 
file  trash.c
 
file  treeIO.c
 
file  treeIO.h [code]
 
file  utils-merge.c
 
file  utils.c
 Miscellaneous general utility and helper functions.