This is the command gainLoss that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 - [email protected]
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)
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