Steep learning curve for those unfamiliar with numerical taxonomy.

| Error Message | Cause | Solution | | :--- | :--- | :--- | | | Math coprocessor emulation bug. | Use a patch like CRT_fix on the NTSYS executable, or run in DOSBox with cputype=pentium . | | “Cannot open GRAPHICS.DEV” | Missing or corrupted device driver. | Copy GRAPHICS.DEV from the original disk to the working directory. | | “Matrix not positive definite” | PCA attempted on a non-invertible similarity matrix. | Use PCoA (principal coordinate) instead, or check for duplicate OTUs. | | “HPGL output empty” | Virtual printer not configured. | Set HPGL output to a file, then use an external converter. |

Another key strength of the software is its versatility in data handling. It supports various data types, including binary data (presence/absence), qualitative data, and quantitative continuous data. This flexibility has made NTSYS pc 2.02 a staple in agricultural research, microbiology, and botany. For instance, plant breeders frequently use the software to analyze genetic diversity among crop varieties, determining which distinct genotypes are best suited for breeding programs to avoid inbreeding and enhance yield.