In this study, we developed a new Skeletal Tone Analysis Tool that can determine the skeletal tones of various melodies and used it to analyze the gayageum, geomungo, daegeum, piri, and haegeum melodies of and to compare the characteristics of the two music. The analysis of music using the Python-based Skeletal Tone Analysis Tool proceeds in the following steps: data input, data post-processing and analysis, determination of Jeonggan representative tones, and determination of skeletal tones. One advantage of this tool is that it provides real-time results after data preparation. Using this tool, we successfully identified the skeletal tones of and . Furthermore, we verified the similarities and differences between the melodies by each instrument through the tone cluster analysis. Based on these results, we discussed the potential applications of the Skeletal Tone Analysis Tool. Firstly, we reaffirmed heterophonic characteristics by visualizing them through the skeletal melody matrix and confirmed the melody structure across different pieces. Secondly, we observed the presence of auxiliary tones around the skeletal tones, with a wider range observed in compared to . Moreover, we discovered that the auxiliary tones around each skeletal tone vary depending on the instrument, deviation from the conventional dichotomy of string and wind instruments. This highlights the unique characteristics of each instrument.