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)