#cped and modified from paramFile_KEGG2013_v2 1/15/2014
_seqFile MOtree_GL/MOtree.GL.011514
_treeFile MOtree_GL/MOprunedtree.newick
_printPij_t 1
_printL_of_Pos 1
_calculateAncestralReconstruct 1
_printAncestralReconstructFullData 1
_printExpPerPosPerBranchMatrix 1
_printTree 1
_optimizationLevel      mid
_rateDistributionType	GAMMA
_performOptimizationsBBL        1
_performOptimizations 1
_numberOfGainCategories 3						
_numberOfLossCategories	3					
_numberOfRateCategories	3
_outDir kegg2013_MOtree_results_TEST 
#_logFile kegg2013_log.txt
_maxNumOfIterationsManyStarts	3
_calculateRate4site     1                                                       
_calculeGainLoss4site   1
_gainLossDist   1
_calculeGainLoss4site   1
_printLikelihoodLandscapeGainLoss       1
_printPij_t     1
#_printP11forgain        1
#_numOfSimulationsForPotExp      1000
#_numberOfPositions2simulate	100000
#_simulatePosteriorExpectationOfChange   0
#_simulateSequences      0
#_isRootFreqEQstationaryInSimulations    1
#_printnodesContentSim   1