BioGem Blog

NTSYSpc (Numerical Taxonomy and Multivariate Analysis System) is a simple and light-weight statistical software used for cluster analysis of molecular genetic qualitative data. The broad features of NTSYSpc include similarity/dissimilarity, clustering, graph theoretic methods, ordination, interactive graphics, multivariate tests, geometric morphometrics, and comparison of matrices. This brief video tutorial illustrates how to use NTSYSpc to create a cladogram ( a tree diagram that shows the cladistic relationship between several populations/species ) from a binary matrix. The table made up of 0s and 1s is represented by the binary matrix. On the other hand, 1 denotes the presence of character, 0 denotes the absence of character ( trait ), and a blank area denotes the absence of character.

This tutorial explains how to perform P rincipal C omponent A nalysis (PCA) and P rincipal C oordinate A nalysis (PCoA) of multivariate data using the NTSYSpc tool. NTSYSpc ( N umerical T axonomy and Multivariate Analysis SYS tem for p ersonal c omputer) is a simple and efficient statistical tool used to find patterns and display structures in multivariate data. The tool used in this tutorial is NTSYSpc v2.11a . In this tutorial, I have used a sample allelic data matrix (shown below). The matrix file consists of molecular weight size marker (rows) and sample/loci (columns). \[M_{mw,s}=\begin{bmatrix}0&0&1&1&0&0\\0&0&1&0&0&0\\0&0&1&1&0&0\\0&0&1&1&1&1\\1&1&1&0&0&0\\0&1&1&1&0&0\\0&0&1&1&1&1\\0&0&0&0&1&1\\1&0&0&0&0&0\\1&1&0&0&0&0\\1&1&0&0&0&0\\0&1&0&0...