You can change the default textitMelting options in the OptionManagement class from the melting.configuration package. There are different default oprions for each type of hybridization.
/** * initialises the DNADefaultOptions HashMap of the * OptionManagement object. */ private void initialisesDNADefaultOptions() { this.DNADefaultOptions.put(NNMethod, "san04"); this.DNADefaultOptions.put(singleMismatchMethod, "allsanpey"); this.DNADefaultOptions.put(tandemMismatchMethod, "allsanpey"); this.DNADefaultOptions.put(internalLoopMethod, "san04"); this.DNADefaultOptions.put(singleDanglingEndMethod, "bom00"); this.DNADefaultOptions.put(doubleDanglingEndMethod, "sugdna02"); this.DNADefaultOptions.put(singleBulgeLoopMethod, "tan04"); this.DNADefaultOptions.put(longDanglingEndMethod, "sugdna02"); this.DNADefaultOptions.put(longBulgeLoopMethod, "san04"); this.DNADefaultOptions.put(approximativeMode, "wetdna91"); this.DNADefaultOptions.put(DMSOCorrection, "ahs01"); this.DNADefaultOptions.put(formamideCorrection, "bla96"); this.DNADefaultOptions.put(inosineMethod, "san05"); this.DNADefaultOptions.put(hydroxyadenineMethod, "sug01"); this.DNADefaultOptions.put(azobenzeneMethod, "asa05"); this.DNADefaultOptions.put(lockedAcidMethod, "mct04"); this.DNADefaultOptions.put(NaEquivalentMethod, "ahs01"); } /** * initialises the RNADefaultOptions HashMap of the * OptionManagement object. */ private void initialiseRNADefaultOptions() { this.RNADefaultOptions.put(NNMethod, "xia98"); this.RNADefaultOptions.put(singleMismatchMethod, "zno07"); this.RNADefaultOptions.put(wobbleBaseMethod, "tur99"); this.RNADefaultOptions.put(tandemMismatchMethod, "tur06"); this.RNADefaultOptions.put(internalLoopMethod, "tur06"); this.RNADefaultOptions.put(singleBulgeLoopMethod, "tur06"); this.RNADefaultOptions.put(longBulgeLoopMethod, "tur06"); this.RNADefaultOptions.put(CNGMethod, "bro05"); this.RNADefaultOptions.put(approximativeMode, "wetrna91"); this.RNADefaultOptions.put(inosineMethod, "zno07"); this.RNADefaultOptions.put(NaEquivalentMethod, "ahs01"); this.RNADefaultOptions.put(DMSOCorrection, "ahs01"); this.RNADefaultOptions.put(formamideCorrection, "bla96"); this.RNADefaultOptions.put(singleDanglingEndMethod, "ser08"); this.RNADefaultOptions.put(doubleDanglingEndMethod, "ser06"); this.RNADefaultOptions.put(longDanglingEndMethod, "sugrna02"); } /** * initialises the hybridDefaultOptions HashMap of the * OptionManagement object. */ private void initialiseHybridDefaultOptions() { this.hybridDefaultOptions.put(NNMethod, "sug95"); this.hybridDefaultOptions.put(approximativeMode, "Wetdnarna91"); this.hybridDefaultOptions.put(NaEquivalentMethod, "ahs01"); this.hybridDefaultOptions.put(DMSOCorrection, "ahs01"); this.hybridDefaultOptions.put(formamideCorrection, "bla96"); } /** * initialises the mRNADefaultOptions HashMap of the * OptionManagement object. */ private void initialiseMRNADefaultOptions() { this.mRNADefaultOptions.put(NNMethod, "tur06"); this.mRNADefaultOptions.put(NaEquivalentMethod, "ahs01"); this.mRNADefaultOptions.put(DMSOCorrection, "ahs01"); this.mRNADefaultOptions.put(formamideCorrection, "bla96"); }