Some of the features include in NTSYSpc are listed below.

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1. Similarity and dissimilarity: correlation, distance, 34 association coefficients, and 11 genetic distance coefficients.
2. Clustering: UPGMA and other hierarchical SAHN methods (allows for ties). Neighbor-joining method (including the new unweighted version). Several types of consensus trees.
3. Graph theoretic methods: minimum-length spanning trees. Graphs (unrooted trees) from the neighbor-joining method.
4. Ordination: principal components & principal coordinates analysis, correspondence analysis, metric & non-metric multidimensional scaling analysis, singular-value decompositions, projections onto axes and Burnaby's method. Canonical variates analysis. Programs for multiple factor analysis, common principal components analysis, partial least-squares, multiple correlation, and canonical correlations are also included.
5. Interactive graphics: phenograms, phylogenetic trees, 2D scatter plots , comparison of dis/similarity matrices, Fourier plots of outlines, Procrustes plots, and 3-D perspective plots.
6. Multivariate tests: canonical variates analysis, tests for homogeneity of covariance matrices, tests for number of dimensions, generalized multivariate multiple regression analysis. There are also provisions for bootstrap, jackknife, and simulation experiments.
7. Geometric morphometrics: includes specialized modules for Procrustes analysis to superimpose landmark configurations, plotting the results of a Procrustes analysis, Fourier analysis (including 2D and 3D elliptic) of outline shapes, plotting outlines and Fourier coefficients, and computation of 2D and 3D partial warp scores and estimates of the uniform component.
8. Other: includes comparison of matrices by cophenetic correlation, Mantel test, 3-way Mantel test, data standardization, and matrix transformations (simple functions, deletion, and now matrix transpose). Matrices can be split or combined.

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