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)