NAME

       gainLoss - Analysis of Phyletic Patterns in a Likelihood Framework

DESCRIPTION

       The  gainLoss  project:  Analysis  of Phyletic Patterns in a Likelihood Framework Version:
       gainLoss.VR01.266 - last updated 14.10.2013 Ofir Cohen - ofircohe@tau.ac.il

USAGE

       use a parameter file with these options:

       _seqFile

       _treeFile

              _rootAt   _logFile   _logValue   _referenceSeq   _outDir   _outFile    _treeOutFile
              _numberOfGainCategories       _numberOfLossCategories       _numberOfRateCategories
              _maxNumOfIterationsModel      _epsilonOptimizationModel      _maxNumOfIterationsBBL
              _epsilonOptimizationBBL _epsilonOptimization

              _gainLossDist   _calculateRate4site  _calculeGainLoss4site  _printTree  _printPij_t
              _printLofPos  _performOptimizations  _isHGT_normal_Pij  _isReversible  ...(a   very
              partial list)