                     ..:: Data files ::..

Data/
  LSU.phy                        Sequence file in phylip format.
  LSU.dnd                        Unrooted tree in newick format.
  LSUrooted.dnd                  Rooted tree in newick format.
  tree.dnd                       A candidate tree.
  treeList.dnd                   A list of trees in newick format.
  treeList2.dnd                  Another list of trees in newick format.
  OutGroup.txt                   A list of taxons to be used with BppReRoot.
  lysozymeLarge.fasta and .dnd   Files from the PAML package.
  Myo.mase                       Myoglobin sequence alignment, From dutheil and Galtier 2007
  HIV1_REF_2010_gag_DNA.fasta    Alignment file downloaded from the HIV database on 21/12/11
  " " _macse                     realigned with Macse 0.8


                   ..:: Options files ::..

These option files are split in their respective program directory:
  Dist.bpp                       BppDist option file.
  Pars.bpp                       BppPars option file.
  ML.bpp                         BppML option file. Homogeneous model. 
  MLNHGG.bpp                     BppML option file. Galtier & Gouy non-homogeneous model, like in the MHNL package.
  MLNH.bpp                       BppML option file. Gemeral non-homogeneous models.
  SeqGen.bpp                     BppSeqGen option file.
  SeqGenHomogeneousModel.bpp     File included by SeqGen.bpp. Not to be used directly.
  SeqGenNonHomogeneousModel.bpp  File included by SeqGen.bpp. Not to be used directly.
  Consense.bpp                   BppConsense option file.
  SeqMan.bpp                     BppSeqMan option file.
  ReRoot.bpp                     BppReRoot option file.
  AlnScores.bpp                  BppAlnscore option file.

