_mainType Optimize_Model
_treeFile model.tree
_characterFile in_chars.fasta
_seqFile in_msa.fasta
_outDir RESULTS
_outFile traitRate.res
_logFile log.txt
_scaledTreeFile scaled.tree
_charModelParam1 0.5
_charModelParam2 5
_gammaParam 0.5
_seqModelParam1 2
_relRate 1
_seqModelType HKY
_logValue 3
_bScaleTree 1
_stochasicMappingIterations 100
_treeLength 1.0