_mainType Optimize_Model
_treeFile FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY/example_Tree.nwc
_characterFile FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY/example_Traits.fas
_seqFile FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY/example_MSA.fas
_outDir FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY/result/
_outFileNullParams FULL_PATH_TO_YOUR_EXAMPLE_DIRECTORY/result/example_nullModelParams.res
_outFile example_results.txt
_logFile example_log.txt
_LLPerPositionFile example_LL_per_pos.txt
_bOptCharModel 1
_bOptProportion 1
_bOptRelRate 1
_bOptSeqModel 1
_bPruneShortestTip 0
_bScaleTree 1
_relRateMaxVal 4
_gammaCategories 4
_gammaParam 1
_globalRate 1
_llCalcType COMBINED
_optimizeIterNum 0,2,5
_optimizePointsNum 30,3,1
_optimizeStrategies 1,1,1
_seqModelType HKY
_stochasicMappingIterations 1000
_bGridStartPoints 1